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Sample records for situ structure-function studies

  1. Two-dimensional boron nitride structures functionalization: first principles studies.

    PubMed

    Ponce-Pérez, R; Cocoletzi, Gregorio H; Takeuchi, Noboru

    2016-09-01

    Density functional theory calculations have been performed to investigate two-dimensional hexagonal boron nitride (2D hBN) structures functionalization with organic molecules. 2x2, 4x4 and 6x6 periodic 2D hBN layers have been considered to interact with acetylene. To deal with the exchange-correlation energy the generalized gradient approximation (GGA) is invoked. The electron-ion interaction is treated with the pseudopotential method. The GGA with the Perdew-Burke-Ernzerhoff (PBE) functionals together with van der Waals interactions are considered to deal with the composed systems. To investigate the functionalization two main configurations have been explored; in one case the molecule interacts with the boron atom and in the other with the nitrogen atom. Results of the adsorption energies indicate chemisorption in both cases. The total density of states (DOS) displays an energy gap in both cases. The projected DOS indicate that the B-p and N-p orbitals are those that make the most important contribution in the valence band and the H-s and C-p orbitals provide an important contribution in the conduction band to the DOS. Provided that the interactions of the acetylene with the 2D layer modify the structural and electronic properties of the hBN the possibility of structural functionalization using organic molecules may be concluded. PMID:27566317

  2. Experimental Studies of Structure, Function, and Coherent Oscillations in Biomolecules

    NASA Astrophysics Data System (ADS)

    Champion, Paul

    2005-03-01

    Femtosecond coherence spectroscopy can be used to prepare and monitor coherent states of biological samples such as heme proteins. Following laser pulse induced ligand photolysis of myoglobin, the (initially planar) heme group is left far from its final product state equilibrium geometry. This leads to coherent oscillations of those modes composing the reaction coordinate for diatomic ligand binding and dissociation. Coherence studies, along with ``white light'' continuum measurements of the spectral dynamics, show that the timescale for diatomic ligand dissociation is much shorter than the 150fs period of the Fe-histidine vibration (the Fe-histidine bond constitutes the sole covalent linkage between the heme and protein material). Recent measurements of the effects of temperature and sample condition on the coherent motions of the heme and on the ultrafast geminate rebinding of various diatomic ligands are also reported. Investigations of heme model compounds, in the absence of the protein material, show that the spectrum of low frequency heme modes can be altered by the choice of sample conditions. The studies of the heme model compounds also allow the diatomic ligand rebinding barrier to be separated into ``proximal'' and ``distal'' contributions that can be separately determined.

  3. Inverse structure functions

    SciTech Connect

    Pearson, Bruce R.; Water, Willem van de

    2005-03-01

    While the ordinary structure function in turbulence is concerned with the statistical moments of the velocity increment {delta}u measured over a distance r, the inverse structure function is related to the distance r where the turbulent velocity exits the interval {delta}u. We study inverse structure functions of wind-tunnel turbulence which covers a range of Reynolds numbers Re{sub {lambda}}=400-1100. We test a recently proposed relation between the scaling exponents of the ordinary structure functions and those of the inverse structure functions [S. Roux and M. H. Jensen, Phys. Rev. E 69, 16309 (2004)]. The relatively large range of Reynolds numbers in our experiment also enables us to address the scaling with Reynolds number that is expected to highlight the intermediate dissipative range. While we firmly establish the (relative) scaling of inverse structure functions, our experimental results fail both predictions. Therefore, the question of the significance of inverse structure functions remains open.

  4. Evolutionary Studies Illuminate the Structural-Functional Model of Plant Phytochromes[W

    PubMed Central

    Mathews, Sarah

    2010-01-01

    A synthesis of insights from functional and evolutionary studies reveals how the phytochrome photoreceptor system has evolved to impart both stability and flexibility. Phytochromes in seed plants diverged into three major forms, phyA, phyB, and phyC, very early in the history of seed plants. Two additional forms, phyE and phyD, are restricted to flowering plants and Brassicaceae, respectively. While phyC, D, and E are absent from at least some taxa, phyA and phyB are present in all sampled seed plants and are the principal mediators of red/far-red–induced responses. Conversely, phyC-E apparently function in concert with phyB and, where present, expand the repertoire of phyB activities. Despite major advances, aspects of the structural-functional models for these photoreceptors remain elusive. Comparative sequence analyses expand the array of locus-specific mutant alleles for analysis by revealing historic mutations that occurred during gene lineage splitting and divergence. With insights from crystallographic data, a subset of these mutants can be chosen for functional studies to test their importance and determine the molecular mechanism by which they might impact light perception and signaling. In the case of gene families, where redundancy hinders isolation of some proportion of the relevant mutants, the approach may be particularly useful. PMID:20118225

  5. Use of Synthetic Peptides to Study Structure-Function Relationships of Matrix Metalloproteinases and Their Substrates.

    NASA Astrophysics Data System (ADS)

    Netzel-Arnett, Sarah Joann

    The matrix metalloproteinases (MMPs) are a family of zinc proteinases that is collectively capable of degrading the major components of the extracellular matrix. A variety of synthetic peptides has been prepared which are models for the human MMP and their substrates to study structure -function relationships in this enzyme-substrate system. To elucidate the sequence specificity of the MMP, the k _{cat}/K_ M values for the hydrolysis of over 50 synthetic octapeptides has been investigated. Similarities, as well as distinct differences have been found between the individual MMP with the largest differences occurring at subsites P_1, P_1^' and P_3 ^'. Based on these data, quenched -fluorescence substrates with optimized sequences have been developed for five human MMP. The key features of these heptapeptides are a tryptophan on the P_ n^' side and a dinitrophenol quenching group on the amino terminus. To assess the role of the triple helical conformation in the collagenase-collagen system, a series of triple helical peptides has been prepared and shown to compete with collagen in collagenase assays. This provides evidence for the existence of a triple helical recognition site distinct from the active site. All of the MMP are secreted as zymogens and it has been postulated that the portion of the propeptide surrounding a critical cysteine is responsible for maintaining latency. Conformational energy calculations and mutagenesis studies have suggested that this region adopts a specific conformation that stabilizes the latent form. Peptide models of this region of the propeptide have been prepared and shown to inhibit the MMP. CD and NMR studies, however, have failed to provide evidence for the predicted peptide conformation. Thus, the observed inhibition may reflect their propensity to adopt the propeptide conformation upon binding to the enzyme.

  6. Genetic and structure-function studies of missense mutations in human endothelial lipase.

    PubMed

    Razzaghi, Hamid; Tempczyk-Russell, Anna; Haubold, Kurt; Santorico, Stephanie A; Shokati, Touraj; Christians, Uwe; Churchill, Mair E A

    2013-01-01

    Endothelial lipase (EL) plays a pivotal role in HDL metabolism. We sought to characterize EL and its interaction with HDL as well as its natural variants genetically, functionally and structurally. We screened our biethnic population sample (n = 802) for selected missense mutations (n = 5) and identified T111I as the only common variant. Multiple linear regression analyses in Hispanic subjects revealed an unexpected association between T111I and elevated LDL-C (p-value = 0.012) and total cholesterol (p-value = 0.004). We examined lipase activity of selected missense mutants (n = 10) and found different impacts on EL function, ranging from normal to complete loss of activity. EL-HDL lipidomic analyses indicated that EL has a defined remodeling of HDL without exhaustion of the substrate and a distinct and preference for several fatty acids that are lipid mediators and known for their potent pro- and anti-inflammatory properties. Structural studies using homology modeling revealed a novel α/β motif in the C-domain, unique to EL. The EL dimer was found to have the flexibility to expand and to bind various sizes of HDL particles. The likely impact of the all known missense mutations (n = 18) on the structure of EL was examined using molecular modeling and the impact they may have on EL lipase activity using a novel structure-function slope based on their structural free energy differences. The results of this multidisciplinary approach delineated the impact of EL and its variants on HDL. Moreover, the results suggested EL to have the capacity to modulate vascular health through its role in fatty acid-based signaling pathways. PMID:23536757

  7. A detailed study of nucleon structure function in nuclei in the valence quark region

    SciTech Connect

    Bianchi, N.

    1994-04-01

    The so called {open_quotes}EMC effect{close_quotes} discovered during the 1980`s, has caused a big controversy in the community of nuclear and high energy physicists; during the last ten years, five experiments have been performed in different laboratories and several hundreds of papers about the possible interpretation of the modification of the nucleon structure function inside nuclei have been published. However, from the experimental point of view, the main goal of four experiments (EMC, BCDMS, NMC, FNAL) has been to emphasize the region of low x{sub b}, where shadowing effects appear. In the region of valence quarks and nuclear effects (x{sub b} > 0.1 - 0.2) the most reliable data presently available are from the SLAC E139 experiment performed in 1983 with only 80 hours of beam time. New precise data in the valence quark region are necessary to measure separate structure functions F{sub 2}(x{sub b}, Q{sup 2}) and R{sup lt}(x{sub b},Q{sup 2}) = {sigma}{sub l}/{sigma}{sub t}, and to investigate the real A-dependence of the ratio between bound and free-nucleon structure functions which is not completely defined by the SLAC data. Moreover, from the nuclear physics point of view, a measurement on some unexplored nuclei, like {sup 3}He and {sup 48}Ca, would be of great interest. The intermediate scaling region (0.1 < x{sub b} < 0.7) would be accessible at CEBAF if the machine energy will reach 6-8 GeV, as suggested by all the tests performed on the RF cavities. This physics program has been already presented in two letter of intents.

  8. Study of neutron spin structure functions at low Q{sup 2} with polarized {sup 3}He

    SciTech Connect

    Seonho Choi

    2000-12-12

    The recently completed experiment E94-010 at Jefferson Lab studies the neutron spin structure functions at low momentum transfer (Q{sup 2}) values. Using a polarized {sup 3} He target and polarized electron beam, we have measured the asymmetries and cross sections for {sup 3}He(e,e') from the elastic to the deep inelastic region. The covered Q{sup 2} ranges from 0.03 to 1.1 GeV{sup 2}. From the data, the Q{sup 2} evolution of the spin structure functions for {sup 3}He and neutron, and of the Gerasimov-Drell-Hearn (GDH) sum rule has been studied, and the preliminary results are presented.

  9. Structure-function studies of the human immunodeficiency virus type 1 matrix protein, p17.

    PubMed

    Cannon, P M; Matthews, S; Clark, N; Byles, E D; Iourin, O; Hockley, D J; Kingsman, S M; Kingsman, A J

    1997-05-01

    The human immunodeficiency virus type 1 (HIV-1) matrix protein, p17, plays important roles in both the early and late stages of the viral life cycle. Using our previously determined solution structure of p17, we have undertaken a rational mutagenesis program aimed at mapping structure-function relationships within the molecule. Amino acids hypothesized to be important for p17 function were mutated and examined for effect in an infectious proviral clone of HIV-1. In parallel, we analyzed by nuclear magnetic resonance spectroscopy the structure of recombinant p17 protein containing such substitutions. These analyses identified three classes of mutants that were defective in viral replication: (i) proteins containing substitutions at internal residues that grossly distorted the structure of recombinant p17 and prevented viral particle formation, (ii) mutations at putative p17 trimer interfaces that allowed correct folding of recombinant protein but produced virus that was defective in particle assembly, and (iii) substitution of basic residues in helix A that caused some relocation of virus assembly to intracellular locations and produced normally budded virions that were completely noninfectious. PMID:9094619

  10. Structural optimization and structure-functional selectivity relationship studies of G protein-biased EP2 receptor agonists.

    PubMed

    Ogawa, Seiji; Watanabe, Toshihide; Moriyuki, Kazumi; Goto, Yoshikazu; Yamane, Shinsaku; Watanabe, Akio; Tsuboi, Kazuma; Kinoshita, Atsushi; Okada, Takuya; Takeda, Hiroyuki; Tani, Kousuke; Maruyama, Toru

    2016-05-15

    The modification of the novel G protein-biased EP2 agonist 1 has been investigated to improve its G protein activity and develop a better understanding of its structure-functional selectivity relationship (SFSR). The optimization of the substituents on the phenyl ring of 1, followed by the inversion of the hydroxyl group on the cyclopentane moiety led to compound 9, which showed a 100-fold increase in its G protein activity compared with 1 without any increase in β-arrestin recruitment. Furthermore, SFSR studies revealed that the combination of meta and para substituents on the phenyl moiety was crucial to the functional selectivity. PMID:27055938

  11. Mutants of Chlamydomonas: tools to study thylakoid membrane structure, function and biogenesis.

    PubMed

    de Vitry, C; Vallon, O

    1999-06-01

    The unicellular green alga Chlamydomonas reinhardtii is a model system for the study of photosynthesis and chloroplast biogenesis. C. reinhardtii has a photosynthesis apparatus similar to that of higher plants and it grows at rapid rate (generation time about 8 h). It is a facultative phototroph, which allows the isolation of mutants unable to perform photosynthesis and its sexual cycle allows a variety of genetic studies. Transformation of the nucleus and chloroplast genomes is easily performed. Gene transformation occurs mainly by homologous recombination in the chloroplast and heterologous recombination in the nucleus. Mutants are precious tools for studies of thylakoid membrane structure, photosynthetic function and assembly. Photosynthesis mutants affected in the biogenesis of a subunit of a protein complex usually lack the entire complex; this pleiotropic effect has been used in the identification of the other subunits, in the attribution of spectroscopic signals and also as a 'genetic cleaning' process which facilitates both protein complex purification, absorption spectroscopy studies or freeze-fracture analysis. The cytochrome b6f complex is not required for the growth of C. reinhardtii, unlike the case of photosynthetic prokaryotes in which the cytochrome complex is also part of the respiratory chain, and can be uniquely studied in Chlamydomonas by genetic approaches. We describe in greater detail the use of Chlamydomonas mutants in the study of this complex. PMID:10433117

  12. Structure-function studies of DNA damage using AB INITIO quantum mechanics and molecular dynamics simulation

    SciTech Connect

    Miller, J.; Miaskiewicz, K.; Osman, R.

    1993-12-01

    Studies of ring-saturated pyrimidine base lesions are used to illustrate an integrated modeling approach that combines quantum-chemical calculations with molecular dynamics simulation. Electronic-structure calculations on the lesions in Isolation reveal strong conformational preferences due to interactions between equatorial substituents to the pyrimidine ring. Large distortions of DNA should result when these interactions force the methyl group of thymine to assume an axial orientation, as is the case for thymine glycol but not for dihydrothymine. Molecular dynamics simulations of the dodecamer d(CGCGAATTCGCG){sub 2} with and without a ring-saturated thymine lesion at position T7 support this conclusion. Implications of these studies for recognition of thymine lesions by endonuclease III are also discussed.

  13. Structural-functional insights and studies on saccharide binding of Sophora japonica seed lectin.

    PubMed

    Yadav, Priya; Shahane, Ganesh; Ramasamy, Sureshkumar; Sengupta, Durba; Gaikwad, Sushama

    2016-10-01

    Functional and conformational transitions of the Sophora japonica seed lectin (SJL) were studied in detail using bioinformatics and biophysical tools. Homology model of the lectin displayed all the characteristics of the legume lectin monomer and the experimental observations correlated well with the structural information. In silico studies were performed by protein-ligand docking, calculating the respective binding energies and the residues involved in the interactions were derived from LigPlot(+) analysis. Fluorescence titrations showed three times higher affinity of T-antigen disaccharide than N-acetyl galactosamine (GalNAc) towards SJL indicating extended sugar binding site of the lectin. Thermodynamic parameters of T-antigen binding to SJL indicated the process to be endothermic and entropically driven while those of GalNAc showed biphasic process. SDS-PAGE showed post-translationally modified homotetrameric species of the lectin under native conditions. In presence of guanidine hydrochloride (0.5-5.0M), the tetramer first dissociated into dimers followed by unfolding of the protein as indicated by size exclusion chromatography, fluorescence and CD spectroscopy. Different structural rearrangements were observed during thermal denaturation of SJL at physiological pH 7.2, native pH 8.5 and molten globule inducing pH 1.0. Topological information revealed by solute quenching studies at respective pH indicated differential hydrophobic environment and charge density around tryptophan residues. PMID:27185070

  14. Structure-function studies of the herpes simplex virus type 1 DNA polymerase.

    PubMed Central

    Haffey, M L; Novotny, J; Bruccoleri, R E; Carroll, R D; Stevens, J T; Matthews, J T

    1990-01-01

    The analysis of the deduced amino acid sequence of the herpes simplex virus type 1 (HSV-1) DNA polymerase reported here suggests that the polymerase structure consists of domains carrying separate biological functions. The HSV-1 enzyme is known to possess 5'-3'-exonuclease (RNase H), 3'-5'-exonuclease, and DNA polymerase catalytic activities. Sequence analysis suggests an arrangement of these activities into distinct domains resembling the organization of Escherichia coli polymerase I. In order to more precisely define the structure and C-terminal limits of a putative catalytic domain responsible for the DNA polymerization activity of the HSV-1 enzyme, we have undertaken in vitro mutagenesis and computer modeling studies of the HSV-1 DNA polymerase gene. Sequence analysis predicts that the major DNA polymerization domain of the HSV-1 enzyme will be contained between residues 690 and 1100, and we present a three-dimensional model of this region, on the basis of the X-ray crystallographic structure of the E. coli polymerase I. Consistent with these structural and modeling studies, deletion analysis by in vitro mutagenesis of the HSV-1 DNA polymerase gene expressed in Saccharomyces cerevisiae has confirmed that certain amino acids from the C terminus (residues 1073 to 1144 and 1177 to 1235) can be deleted without destroying HSV-1 DNA polymerase catalytic activity and that the extreme N-terminal 227 residues are also not required for this activity. Images PMID:2168983

  15. Preparation of Protein Samples for NMR Structure, Function, and Small Molecule Screening Studies

    PubMed Central

    Acton, Thomas B.; Xiao, Rong; Anderson, Stephen; Aramini, James; Buchwald, William A.; Ciccosanti, Colleen; Conover, Ken; Everett, John; Hamilton, Keith; Huang, Yuanpeng Janet; Janjua, Haleema; Kornhaber, Gregory; Lau, Jessica; Lee, Dong Yup; Liu, Gaohua; Maglaqui, Melissa; Ma, Lichung; Mao, Lei; Patel, Dayaban; Rossi, Paolo; Sahdev, Seema; Shastry, Ritu; Swapna, G.V.T.; Tang, Yeufeng; Tong, Saichiu; Wang, Dongyan; Wang, Huang; Zhao, Li; Montelione, Gaetano T.

    2014-01-01

    In this chapter, we concentrate on the production of high quality protein samples for NMR studies. In particular, we provide an in-depth description of recent advances in the production of NMR samples and their synergistic use with recent advancements in NMR hardware. We describe the protein production platform of the Northeast Structural Genomics Consortium, and outline our high-throughput strategies for producing high quality protein samples for nuclear magnetic resonance (NMR) studies. Our strategy is based on the cloning, expression and purification of 6X-His-tagged proteins using T7-based Escherichia coli systems and isotope enrichment in minimal media. We describe 96-well ligation-independent cloning and analytical expression systems, parallel preparative scale fermentation, and high-throughput purification protocols. The 6X-His affinity tag allows for a similar two-step purification procedure implemented in a parallel high-throughput fashion that routinely results in purity levels sufficient for NMR studies (> 97% homogeneity). Using this platform, the protein open reading frames of over 17,500 different targeted proteins (or domains) have been cloned as over 28,000 constructs. Nearly 5,000 of these proteins have been purified to homogeneity in tens of milligram quantities (see Summary Statistics, http://nesg.org/statistics.html), resulting in more than 950 new protein structures, including more than 400 NMR structures, deposited in the Protein Data Bank. The Northeast Structural Genomics Consortium pipeline has been effective in producing protein samples of both prokaryotic and eukaryotic origin. Although this paper describes our entire pipeline for producing isotope-enriched protein samples, it focuses on the major updates introduced during the last 5 years (Phase 2 of the National Institute of General Medical Sciences Protein Structure Initiative). Our advanced automated and/or parallel cloning, expression, purification, and biophysical screening

  16. Structural, functional and optical studies on the amino acid doped glycine crystal

    NASA Astrophysics Data System (ADS)

    Manikandan, M. R.; Mahalingam, T.; Ravi, G.

    2012-06-01

    Single crystals of pure and amino acid (L-arginine) doped γ-glycine single crystals have been grown from aqueous solution by employing slow evaporation method. Morphological changes in different crystallographic planes were observed in the L-arginine doped γ-glycine crystals. Incorporation of L-arginine was confirmed qualitatively by FTIR spectroscopy. Powder X-ray diffraction was carried out to confirm γ-glycine and assess the single phase nature of the crystals. The lower cutoff wavelength was decreased by the influence of L-arginine in γ-glycine and this leads to an increase in the band gap. Nonlinear optical study revealed that L-arginine doping increases the SHG efficiency of the glycine crystal.

  17. Structure-Functional Study of Tyrosine and Methionine Dipeptides: An Approach to Antioxidant Activity Prediction

    PubMed Central

    Torkova, Anna; Koroleva, Olga; Khrameeva, Ekaterina; Fedorova, Tatyana; Tsentalovich, Mikhail

    2015-01-01

    Quantum chemical methods allow screening and prediction of peptide antioxidant activity on the basis of known experimental data. It can be used to design the selective proteolysis of protein sources in order to obtain products with antioxidant activity. Molecular geometry and electronic descriptors of redox-active amino acids, as well as tyrosine and methionine-containing dipeptides, were studied by Density Functional Theory method. The calculated data was used to reveal several descriptors responsible for the antioxidant capacities of the model compounds based on their experimentally obtained antioxidant capacities against ABTS (2,2′-Azino-bis-(3-ethyl-benzothiazoline-6-sulfonate)) and peroxyl radical. A formula to predict antioxidant activity of peptides was proposed. PMID:26512651

  18. Structure-Functional Study of Tyrosine and Methionine Dipeptides: An Approach to Antioxidant Activity Prediction.

    PubMed

    Torkova, Anna; Koroleva, Olga; Khrameeva, Ekaterina; Fedorova, Tatyana; Tsentalovich, Mikhail

    2015-01-01

    Quantum chemical methods allow screening and prediction of peptide antioxidant activity on the basis of known experimental data. It can be used to design the selective proteolysis of protein sources in order to obtain products with antioxidant activity. Molecular geometry and electronic descriptors of redox-active amino acids, as well as tyrosine and methionine-containing dipeptides, were studied by Density Functional Theory method. The calculated data was used to reveal several descriptors responsible for the antioxidant capacities of the model compounds based on their experimentally obtained antioxidant capacities against ABTS (2,2'-Azino-bis-(3-ethyl-benzothiazoline-6-sulfonate)) and peroxyl radical. A formula to predict antioxidant activity of peptides was proposed. PMID:26512651

  19. Structure-Function Study of Tertiary Amines as Switchable Polarity Solvents

    SciTech Connect

    Aaron D. Wilson; Frederick F. Stewart

    2014-02-01

    A series of tertiary amines have been screened for their function as switchable polarity solvents (SPS). The relative ratios of tertiary amine and carbonate species as well as maximum possible concentration were determined through quantitative 1H and 13C NMR spectroscopy. The viscosities of the polar SPS solutions were measured and ranged from near water in dilute systems through to gel formation at high concentrations. The van't Hoff indices for SPS solutions were measured through freezing point depression studies as a proxy for osmotic pressures. A new form of SPS with an amine : carbonate ratio significantly greater than unity has been identified. Tertiary amines that function as SPS at ambient pressures appear to be limited to molecules with fewer than 12 carbons. The N,N-dimethyl-n-alkylamine structure has been identified as important to the function of an SPS.

  20. The application of psoralens to the study of DNA structure, function and dynamics

    SciTech Connect

    Spielmann, P.H. |

    1991-04-01

    A series of six nitroxide spin-labeled psoralens were designed, synthesized and tested as probes for DNA dynamics. The synthesis of these spin-labeled psoralen derivatives and their photoreactivity with double-stranded DNA fragments is described. The spin labels (nitroxides) were demonstrated to survive the uv irradiation required to bind the probe to the target DNA. EPR spectra of the photobound spin-labels indicate that they do not wobble with respect to the DNA on the time-scales investigated. The author has used psoralen modified DNA as a model for the study of DNA repair enzyme systems in human cell free extracts. He has shown that damage-induced DNA synthesis is associated with removal of psoralen adducts and therefore is {open_quotes}repair synthesis{close_quotes} and not an aberrant DNA synthesis reaction potentiated by deformation of the DNA by adducts. He has found that all DNA synthesis induced by psoralen monoadducts is the consequence of removal of these adducts. By the same approach he has obtained evidence that this in vitro system is capable of removing psoralen cross-links as well. Reported here are synthetic methods that make use of high intensity lasers coupled with HPLC purification to make homogeneous and very pure micromole quantities of furan-side monoadducted, cross-linked, and pyrone-side monoadducted DNA oligonucleotide. These molecules are currently being studied by NMR and X-ray crystallography. The application of the site-specifically psoralen modified oligonucleotide synthesized by these methods to the construction of substrates for the investigation of DNA repair is also discussed.

  1. Structure-function studies of the magnetite-biomineralizing magnetosome-associated protein MamC.

    PubMed

    Nudelman, Hila; Valverde-Tercedor, Carmen; Kolusheva, Sofiya; Perez Gonzalez, Teresa; Widdrat, Marc; Grimberg, Noam; Levi, Hilla; Nelkenbaum, Or; Davidov, Geula; Faivre, Damien; Jimenez-Lopez, Concepcion; Zarivach, Raz

    2016-06-01

    Magnetotactic bacteria are Gram-negative bacteria that navigate along geomagnetic fields using the magnetosome, an organelle that consists of a membrane-enveloped magnetic nanoparticle. Magnetite formation and its properties are controlled by a specific set of proteins. MamC is a small magnetosome-membrane protein that is known to be active in iron biomineralization but its mechanism has yet to be clarified. Here, we studied the relationship between the MamC magnetite-interaction loop (MIL) structure and its magnetite interaction using an inert biomineralization protein-MamC chimera. Our determined structure shows an alpha-helical fold for MamC-MIL with highly charged surfaces. Additionally, the MamC-MIL induces the formation of larger magnetite crystals compared to protein-free and inert biomineralization protein control experiments. We suggest that the connection between the MamC-MIL structure and the protein's charged surfaces is crucial for magnetite binding and thus for the size control of the magnetite nanoparticles. PMID:26970040

  2. Facilitating Structure-Function Studies of CFTR Modulator Sites with Efficiencies in Mutagenesis and Functional Screening.

    PubMed

    Molinski, Steven V; Ahmadi, Saumel; Hung, Maurita; Bear, Christine E

    2015-12-01

    There are nearly 2000 mutations in the CFTR gene associated with cystic fibrosis disease, and to date, the only approved drug, Kalydeco, has been effective in rescuing the functional expression of a small subset of these mutant proteins with defects in channel activation. However, there is currently an urgent need to assess other mutations for possible rescue by Kalydeco, and further, definition of the binding site of such modulators on CFTR would enhance our understanding of the mechanism of action of such therapeutics. Here, we describe a simple and rapid one-step PCR-based site-directed mutagenesis method to generate mutations in the CFTR gene. This method was used to generate CFTR mutants bearing deletions (p.Gln2_Trp846del, p.Ser700_Asp835del, p.Ile1234_Arg1239del) and truncation with polyhistidine tag insertion (p.Glu1172-3Gly-6-His*), which either recapitulate a disease phenotype or render tools for modulator binding site identification, with subsequent evaluation of drug responses using a high-throughput (384-well) membrane potential-sensitive fluorescence assay of CFTR channel activity within a 1 wk time frame. This proof-of-concept study shows that these methods enable rapid and quantitative comparison of multiple CFTR mutants to emerging drugs, facilitating future large-scale efforts to stratify mutants according to their "theratype" or most promising targeted therapy. PMID:26385858

  3. Deuterium Labeling Strategies for Creating Contrast in Structure-Function Studies of Model Bacterial Outer Membranes Using Neutron Reflectometry.

    PubMed

    Le Brun, Anton P; Clifton, Luke A; Holt, Stephen A; Holden, Peter J; Lakey, Jeremy H

    2016-01-01

    Studying the outer membrane of Gram-negative bacteria is challenging due to the complex nature of its structure. Therefore, simplified models are required to undertake structure-function studies of processes that occur at the outer membrane/fluid interface. Model membranes can be created by immobilizing bilayers to solid supports such as gold or silicon surfaces, or as monolayers on a liquid support where the surface pressure and fluidity of the lipids can be controlled. Both model systems are amenable to having their structure probed by neutron reflectometry, a technique that provides a one-dimensional depth profile through a membrane detailing its thickness and composition. One of the strengths of neutron scattering is the ability to use contrast matching, allowing molecules containing hydrogen and those enriched with deuterium to be highlighted or matched out against the bulk isotopic composition of the solvent. Lipopolysaccharides, a major component of the outer membrane, can be isolated for incorporation into model membranes. Here, we describe the deuteration of lipopolysaccharides from rough strains of Escherichia coli for incorporation into model outer membranes, and how the use of deuterated materials enhances structural analysis of model membranes by neutron reflectometry. PMID:26791981

  4. In Situ Vitrification Treatability Study Work Plan

    SciTech Connect

    Charboneau, B.L.; Landon, J.L.

    1989-03-01

    The Buried Waste Program was established in October, 1987 to accelerate the studies needed to develop a recommended long-term management plan for the buried mixed waste at the Radioactive Waste Management Complex at the Idaho National Engineering Laboratory. The In Situ Vitrification Project is being conducted in a Comprehensive Environmental Response, Compensation, and Liability Act Feasibility Study format to identify methods for the long-term management of the mixed waste buried. This In Situ Vitrification Treatability Study Work Plan gives a brief description of the site, work breakdown structure, and project organization: the in situ vitrification technology; the purpose of the tests and demonstrations; and the equipment and materials required for the tests and demonstration. 5 refs., 6 figs., 3 tabs.

  5. Microfluidic neurite guidance to study structure-function relationships in topologically-complex population-based neural networks

    NASA Astrophysics Data System (ADS)

    Honegger, Thibault; Thielen, Moritz I.; Feizi, Soheil; Sanjana, Neville E.; Voldman, Joel

    2016-06-01

    The central nervous system is a dense, layered, 3D interconnected network of populations of neurons, and thus recapitulating that complexity for in vitro CNS models requires methods that can create defined topologically-complex neuronal networks. Several three-dimensional patterning approaches have been developed but none have demonstrated the ability to control the connections between populations of neurons. Here we report a method using AC electrokinetic forces that can guide, accelerate, slow down and push up neurites in un-modified collagen scaffolds. We present a means to create in vitro neural networks of arbitrary complexity by using such forces to create 3D intersections of primary neuronal populations that are plated in a 2D plane. We report for the first time in vitro basic brain motifs that have been previously observed in vivo and show that their functional network is highly decorrelated to their structure. This platform can provide building blocks to reproduce in vitro the complexity of neural circuits and provide a minimalistic environment to study the structure-function relationship of the brain circuitry.

  6. Microfluidic neurite guidance to study structure-function relationships in topologically-complex population-based neural networks

    PubMed Central

    Honegger, Thibault; Thielen, Moritz I.; Feizi, Soheil; Sanjana, Neville E.; Voldman, Joel

    2016-01-01

    The central nervous system is a dense, layered, 3D interconnected network of populations of neurons, and thus recapitulating that complexity for in vitro CNS models requires methods that can create defined topologically-complex neuronal networks. Several three-dimensional patterning approaches have been developed but none have demonstrated the ability to control the connections between populations of neurons. Here we report a method using AC electrokinetic forces that can guide, accelerate, slow down and push up neurites in un-modified collagen scaffolds. We present a means to create in vitro neural networks of arbitrary complexity by using such forces to create 3D intersections of primary neuronal populations that are plated in a 2D plane. We report for the first time in vitro basic brain motifs that have been previously observed in vivo and show that their functional network is highly decorrelated to their structure. This platform can provide building blocks to reproduce in vitro the complexity of neural circuits and provide a minimalistic environment to study the structure-function relationship of the brain circuitry. PMID:27328705

  7. Microfluidic neurite guidance to study structure-function relationships in topologically-complex population-based neural networks.

    PubMed

    Honegger, Thibault; Thielen, Moritz I; Feizi, Soheil; Sanjana, Neville E; Voldman, Joel

    2016-01-01

    The central nervous system is a dense, layered, 3D interconnected network of populations of neurons, and thus recapitulating that complexity for in vitro CNS models requires methods that can create defined topologically-complex neuronal networks. Several three-dimensional patterning approaches have been developed but none have demonstrated the ability to control the connections between populations of neurons. Here we report a method using AC electrokinetic forces that can guide, accelerate, slow down and push up neurites in un-modified collagen scaffolds. We present a means to create in vitro neural networks of arbitrary complexity by using such forces to create 3D intersections of primary neuronal populations that are plated in a 2D plane. We report for the first time in vitro basic brain motifs that have been previously observed in vivo and show that their functional network is highly decorrelated to their structure. This platform can provide building blocks to reproduce in vitro the complexity of neural circuits and provide a minimalistic environment to study the structure-function relationship of the brain circuitry. PMID:27328705

  8. Structure function monitor

    SciTech Connect

    McGraw, John T.; Zimmer, Peter C.; Ackermann, Mark R.

    2012-01-24

    Methods and apparatus for a structure function monitor provide for generation of parameters characterizing a refractive medium. In an embodiment, a structure function monitor acquires images of a pupil plane and an image plane and, from these images, retrieves the phase over an aperture, unwraps the retrieved phase, and analyzes the unwrapped retrieved phase. In an embodiment, analysis yields atmospheric parameters measured at spatial scales from zero to the diameter of a telescope used to collect light from a source.

  9. The Neutron Structure Function

    NASA Astrophysics Data System (ADS)

    Holt, Roy

    2013-10-01

    Knowledge of the neutron structure function is important for testing models of the nucleon, for a complete understanding of deep inelastic scattering (DIS) from nuclei, and for high energy experiments. As there exist no free neutron targets, neutron structure functions have been determined from deep inelastic scattering from the deuteron. Unfortunately, the short-range part of the deuteron wave function becomes important in extracting the neutron structure function at very high Bjorken x. New methods have been devised for Jefferson Lab experiments to mitigate this problem. The BONUS experiment involves tagging spectator neutrons in the deuteron, while the MARATHON experiment minimizes nuclear structure effects by a comparison of DIS from 3H and 3He. A summary of the status and future plans will be presented. This work supported by the U. S. Department of Energy, Office of Nuclear Physics, under contract DE-AC02-06CH11357.

  10. Atomic force microscopy study of the structure function relationships of the biofilm-forming bacterium Streptococcus mutans

    NASA Astrophysics Data System (ADS)

    Cross, Sarah E.; Kreth, Jens; Zhu, Lin; Qi, Fengxia; Pelling, Andrew E.; Shi, Wenyuan; Gimzewski, James K.

    2006-02-01

    Atomic force microscopy (AFM) has garnered much interest in recent years for its ability to probe the structure, function and cellular nanomechanics inherent to specific biological cells. In particular, we have used AFM to probe the important structure-function relationships of the bacterium Streptococcus mutans. S. mutans is the primary aetiological agent in human dental caries (tooth decay), and is of medical importance due to the virulence properties of these cells in biofilm initiation and formation, leading to increased tolerance to antibiotics. We have used AFM to characterize the unique surface structures of distinct mutants of S. mutans. These mutations are located in specific genes that encode surface proteins, thus using AFM we have resolved characteristic surface features for mutant strains compared to the wild type. Ultimately, our characterization of surface morphology has shown distinct differences in the local properties displayed by various S. mutans strains on the nanoscale, which is imperative for understanding the collective properties of these cells in biofilm formation.

  11. Study of the polarized structure functions of the neutron at low Q**2 using polarized He-3

    SciTech Connect

    S.H. Choi

    2004-06-02

    We have measured the electron-He-3 longitudinal and transverse spin dependent inclusive cross sections {pol}He-3({pol}e, e-prime), mostly in the resonance region (up to W ~ 2.5 GeV), over a wide range of four-momentum transfer (Q**2 = 0.03 - 1GeV**2). The longitudinally polarized electron beam of energy ranging from 0.86 to 5.1 GeV of the Jefferson Lab was scattered at a fixed angle of 15.5 degrees, on a high pressure polarized He-3 target in Hall A. The spin dependent structure functions g_1(x), g_2(x) have been extracted and their moments were evaluated. The GDH integral shows dramatic transition from large Q**2 domain to low Q**2 domain in the Burkhardt-Cottingham sum rule for g_2 seems to hold within experimental errors. d_2 is quite large and positive consistent with the SLAC data but at odds with lattice QCD calculation.

  12. Quantum Monte Carlo estimation of complex-time correlations for the study of the ground-state dynamic structure function.

    PubMed

    Rota, R; Casulleras, J; Mazzanti, F; Boronat, J

    2015-03-21

    We present a method based on the path integral Monte Carlo formalism for the calculation of ground-state time correlation functions in quantum systems. The key point of the method is the consideration of time as a complex variable whose phase δ acts as an adjustable parameter. By using high-order approximations for the quantum propagator, it is possible to obtain Monte Carlo data all the way from purely imaginary time to δ values near the limit of real time. As a consequence, it is possible to infer accurately the spectral functions using simple inversion algorithms. We test this approach in the calculation of the dynamic structure function S(q, ω) of two one-dimensional model systems, harmonic and quartic oscillators, for which S(q, ω) can be exactly calculated. We notice a clear improvement in the calculation of the dynamic response with respect to the common approach based on the inverse Laplace transform of the imaginary-time correlation function. PMID:25796238

  13. Spin structure functions

    SciTech Connect

    Jian-ping Chen, Alexandre Deur, Sebastian Kuhn, Zein-eddine Meziani

    2011-06-01

    Spin-dependent observables have been a powerful tool to probe the internal structure of the nucleon and to understand the dynamics of the strong interaction. Experiments involving spin degrees of freedom have often brought out surprises and puzzles. The so-called "spin crisis" in the 1980s revealed the limitation of naive quark-parton models and led to intensive worldwide efforts, both experimental and theoretical, to understand the nucleon spin structure. With high intensity and high polarization of both the electron beam and targets, Jefferson Lab has the world's highest polarized luminosity and the best figure-of-merit for precision spin structure measurements. It has made a strong impact in this subfield of research. This chapter will highlight Jefferson Lab's unique contributions in the measurements of valence quark spin distributions, in the moments of spin structure functions at low to intermediate Q2, and in the transverse spin structure.

  14. A study of nuclear effect in F{sub 3} structure function in the deep inelastic v(v-bar) reactions in nuclei

    SciTech Connect

    Athar, M. Sajjad; Singh, S. K.; Simo, I. Ruiz; Vacas, M. J. Vicente

    2009-11-25

    We study nuclear effect in the F{sub 3}{sup A}(x) structure function in the deep inelastic neutrino reactions on iron by taking into account Fermi motion, binding, target mass correction, shadowing and anti-shadowing corrections. Calculations have been done in a local density approximation using relativistic nuclear spectral functions which include nucleon correlations for nuclear matter. Results for F{sub 3}{sup A}(x) have been compared with the results reported at NuTeV and also with some of the older experiments reported in the literature.

  15. LONG TERM IN SITU DISPOSAL ENGINEERING STUDY

    SciTech Connect

    ADAMS; CARLSON; BROCKMAN

    2003-07-23

    Patent application pulled per Ken Norris (FH General Counsel). The objective of this study is to devise methods, produce conceptual designs, examine and select alternatives, and estimate costs for the demonstration of long-term (300-year) in situ disposal of an existing waste disposal site. The demonstration site selected is the 216-A-24 Crib near the 200 East Area. The site contains a fission product inventory and has experienced plant, animal, and inadvertent than intrusion. Of the potential intrusive events and transport pathways at the site, potential human intrusion has been given primary consideration in barrier design. Intrusion by wind, plants, and animals has been given secondary consideration. Groundwater modeling for a number of barrier configurations has been carried out to help select a barrier that will minimize water infiltration and waste/water contact time. The estimated effective lifetime and cost of 20 barrier schemes, using a variety of materials, have been evaluated. The schemes studied include single component surface barriers, multicomponent barriers, and massively injected grout barriers. Five barriers with high estimated effective lifetimes and relatively low costs have been selected for detailed evaluation. They are basalt riprap barriers, massive soil barriers, salt basin barriers, multi-component fine/coarse barriers, and cemented basalt barriers. A variety of materials and configurations for marking the site have also been considered. A decision analysis was completed to select a barrier scheme for demonstration. The analysis indicated that the basalt riprap alternative would be the preferred choice for a full-scale demonstration. The recommended approach is to demonstrate the basalt riprap barrier at the 216-A-24 Crib as soon as possible. Methods and costs of assessing effectiveness of the demonstration are also described. Preliminary design modifications and costs for applying the five selected barrier schemes to other site types are

  16. Using Case Studies as a Semester-Long Tool to Teach Neuroanatomy and Structure-Function Relationships to Undergraduates

    PubMed Central

    Kennedy, Susan

    2013-01-01

    In addition to being inherently interesting to students, case studies can serve as useful tools to teach neuroanatomy and demonstrate important relationships between brain structure and function. In most undergraduate courses, however, neuroanatomy is presented to students as a “unit” or chapter, much like other topics (e.g., receptors, pharmacology) covered in the course, over a period of a week or two. In this article, a relatively simple model of teaching neuroanatomy is described in which students are actively engaged in the presentation and discussion of case studies throughout the semester, following a general introduction to the structure of the nervous system. In this way, the teaching of neuroanatomy is “distributed” throughout the semester and put into a more user-friendly context for students as additional topics are introduced. Generally, students report enjoying learning brain structure using this method, and commented positively on the class activities associated with learning brain anatomy. Advantages and disadvantages of such a model are presented, as are suggestions for implementing similar models of undergraduate neuroanatomy education. PMID:24319386

  17. Structure-function Studies of Nucleocytoplasmic Transport of Retroviral Genomic RNA by mRNA Export Factor TAP

    SciTech Connect

    M Teplova; L Wohlbold; N Khin; E Izaurralde; D Patel

    2011-12-31

    mRNA export is mediated by the TAP-p15 heterodimer, which belongs to the family of NTF2-like export receptors. TAP-p15 heterodimers also bind to the constitutive transport element (CTE) present in simian type D retroviral RNAs, and they mediate the export of viral unspliced RNAs to the host cytoplasm. We have solved the crystal structure of the RNA recognition and leucine-rich repeat motifs of TAP bound to one symmetrical half of the CTE RNA. L-shaped conformations of protein and RNA are involved in a mutual molecular embrace on complex formation. We have monitored the impact of structure-guided mutations on binding affinities in vitro and transport assays in vivo. Our studies define the principles by which CTE RNA subverts the mRNA export receptor TAP, thereby facilitating the nuclear export of viral genomic RNAs, and, more generally, provide insights on cargo RNA recognition by mRNA export receptors.

  18. Structure, function and management of semi-natural habitats for conservation biological control: a review of European studies.

    PubMed

    Holland, John M; Bianchi, Felix Jja; Entling, Martin H; Moonen, Anna-Camilla; Smith, Barbara M; Jeanneret, Philippe

    2016-09-01

    Different semi-natural habitats occur on farmland, and it is the vegetation's traits and structure that subsequently determine their ability to support natural enemies and their associated contribution to conservation biocontrol. New habitats can be created and existing ones improved with agri-environment scheme funding in all EU member states. Understanding the contribution of each habitat type can aid the development of conservation control strategies. Here we review the extent to which the predominant habitat types in Europe support natural enemies, whether this results in enhanced natural enemy densities in the adjacent crop and whether this leads to reduced pest densities. Considerable variation exists in the available information for the different habitat types and trophic levels. Natural enemies within each habitat were the most studied, with less information on whether they were enhanced in adjacent fields, while their impact on pests was rarely investigated. Most information was available for woody and herbaceous linear habitats, yet not for woodland which can be the most common semi-natural habitat in many regions. While the management and design of habitats offer potential to stimulate conservation biocontrol, we also identified knowledge gaps. A better understanding of the relationship between resource availability and arthropod communities across habitat types, the spatiotemporal distribution of resources in the landscape and interactions with other factors that play a role in pest regulation could contribute to an informed management of semi-natural habitats for biocontrol. © 2016 Society of Chemical Industry. PMID:27178745

  19. Structure Function Studies of Vaccinia Virus Host Range Protein K1 Reveal a Novel Functional Surface for Ankyrin Repeat Proteins▿

    PubMed Central

    Li, Yongchao; Meng, Xiangzhi; Xiang, Yan; Deng, Junpeng

    2010-01-01

    Poxvirus host tropism at the cellular level is regulated by virus-encoded host range proteins acting downstream of virus entry. The functioning mechanisms of most host range proteins are unclear, but many contain multiple ankyrin (ANK) repeats, a motif that is known for ligand interaction through a concave surface. We report here the crystal structure of one of the ANK repeat-containing host range proteins, the vaccinia virus K1 protein. The structure, at a resolution of 2.3 Å, showed that K1 consists entirely of ANK repeats, including seven complete ones and two incomplete ones, one each at the N and C terminus. Interestingly, Phe82 and Ser83, which were previously shown to be critical for K1's function, are solvent exposed and located on a convex surface, opposite the consensus ANK interaction surface. The importance of this convex surface was further supported by our additional mutagenesis studies. We found that K1's host range function was negatively affected by substitution of either Asn51 or Cys47 and completely abolished by substitution of both residues. Cys47 and Asn51 are also exposed on the convex surface, spatially adjacent to Phe82 and Ser83. Altogether, our data showed that K1 residues on a continuous convex ANK repeat surface are critical for the host range function, suggesting that K1 functions through ligand interaction and does so with a novel ANK interaction surface. PMID:20089642

  20. Structure-function studies of a Melanocarpus albomyces laccase suggest a pathway for oxidation of phenolic compounds.

    PubMed

    Kallio, J P; Auer, S; Jänis, J; Andberg, M; Kruus, K; Rouvinen, J; Koivula, A; Hakulinen, N

    2009-10-01

    Melanocarpus albomyces laccase crystals were soaked with 2,6-dimethoxyphenol, a common laccase substrate. Three complex structures from different soaking times were solved. Crystal structures revealed the binding of the original substrate and adducts formed by enzymatic oxidation of the substrate. The dimeric oxidation products were identified by mass spectrometry. In the crystals, a 2,6-dimethoxy-p-benzoquinone and a C-O dimer were observed, whereas a C-C dimer was the main product identified by mass spectrometry. Crystal structures demonstrated that the substrate and/or its oxidation products were bound in the pocket formed by residues Ala191, Pro192, Glu235, Leu363, Phe371, Trp373, Phe427, Leu429, Trp507 and His508. Substrate and adducts were hydrogen-bonded to His508, one of the ligands of type 1 copper. Therefore, this surface-exposed histidine most likely has a role in electron transfer by laccases. Based on our mutagenesis studies, the carboxylic acid residue Glu235 at the bottom of the binding site pocket is also crucial in the oxidation of phenolics. Glu235 may be responsible for the abstraction of a proton from the OH group of the substrate and His508 may extract an electron. In addition, crystal structures revealed a secondary binding site formed through weak dimerization in M. albomyces laccase molecules. This binding site most likely exists only in crystals, when the Phe427 residues are packed against each other. PMID:19563811

  1. Combining wet and dry research: experience with model development for cardiac mechano-electric structure-function studies.

    PubMed

    Quinn, T Alexander; Kohl, Peter

    2013-03-15

    Since the development of the first mathematical cardiac cell model 50 years ago, computational modelling has become an increasingly powerful tool for the analysis of data and for the integration of information related to complex cardiac behaviour. Current models build on decades of iteration between experiment and theory, representing a collective understanding of cardiac function. All models, whether computational, experimental, or conceptual, are simplified representations of reality and, like tools in a toolbox, suitable for specific applications. Their range of applicability can be explored (and expanded) by iterative combination of 'wet' and 'dry' investigation, where experimental or clinical data are used to first build and then validate computational models (allowing integration of previous findings, quantitative assessment of conceptual models, and projection across relevant spatial and temporal scales), while computational simulations are utilized for plausibility assessment, hypotheses-generation, and prediction (thereby defining further experimental research targets). When implemented effectively, this combined wet/dry research approach can support the development of a more complete and cohesive understanding of integrated biological function. This review illustrates the utility of such an approach, based on recent examples of multi-scale studies of cardiac structure and mechano-electric function. PMID:23334215

  2. Structure-function studies of STAR family Quaking proteins bound to their in vivo RNA target sites

    SciTech Connect

    Teplova, Marianna; Hafner, Markus; Teplov, Dmitri; Essig, Katharina; Tuschl, Thomas; Patel, Dinshaw J.

    2013-09-27

    Mammalian Quaking (QKI) and its Caenorhabditis elegans homolog, GLD-1 (defective in germ line development), are evolutionarily conserved RNA-binding proteins, which post-transcriptionally regulate target genes essential for developmental processes and myelination. We present X-ray structures of the STAR (signal transduction and activation of RNA) domain, composed of Qua1, K homology (KH), and Qua2 motifs of QKI and GLD-1 bound to high-affinity in vivo RNA targets containing YUAAY RNA recognition elements (RREs). The KH and Qua2 motifs of the STAR domain synergize to specifically interact with bases and sugar-phosphate backbones of the bound RRE. Qua1-mediated homodimerization generates a scaffold that enables concurrent recognition of two RREs, thereby plausibly targeting tandem RREs present in many QKI-targeted transcripts. Structure-guided mutations reduced QKI RNA-binding affinity in vitro and in vivo, and expression of QKI mutants in human embryonic kidney cells (HEK293) significantly decreased the abundance of QKI target mRNAs. Overall, our studies define principles underlying RNA target selection by STAR homodimers and provide insights into the post-transcriptional regulatory function of mammalian QKI proteins.

  3. Structure Function Studies of Vaccinia Virus Host Range Protein K1 Reveal a Novel Functional Surface for Ankyrin Repeat Proteins

    SciTech Connect

    Li, Yongchao; Meng, Xiangzhi; Xiang, Yan; Deng, Junpeng

    2010-06-15

    Poxvirus host tropism at the cellular level is regulated by virus-encoded host range proteins acting downstream of virus entry. The functioning mechanisms of most host range proteins are unclear, but many contain multiple ankyrin (ANK) repeats, a motif that is known for ligand interaction through a concave surface. We report here the crystal structure of one of the ANK repeat-containing host range proteins, the vaccinia virus K1 protein. The structure, at a resolution of 2.3 {angstrom}, showed that K1 consists entirely of ANK repeats, including seven complete ones and two incomplete ones, one each at the N and C terminus. Interestingly, Phe82 and Ser83, which were previously shown to be critical for K1's function, are solvent exposed and located on a convex surface, opposite the consensus ANK interaction surface. The importance of this convex surface was further supported by our additional mutagenesis studies. We found that K1's host range function was negatively affected by substitution of either Asn51 or Cys47 and completely abolished by substitution of both residues. Cys47 and Asn51 are also exposed on the convex surface, spatially adjacent to Phe82 and Ser83. Altogether, our data showed that K1 residues on a continuous convex ANK repeat surface are critical for the host range function, suggesting that K1 functions through ligand interaction and does so with a novel ANK interaction surface.

  4. Structure-function studies on bacteriorhodopsin. IX. Substitutions of tryptophan residues affect protein-retinal interactions in bacteriorhodopsin

    SciTech Connect

    Mogi, T.; Marti, T.; Khorana, H.G. )

    1989-08-25

    Bacteriorhodopsin contains 8 tryptophan residues distributed across the membrane-embedded helices. To study their possible functions, we have replaced them one at a time by phenylalanine; in addition, Trp-137 and -138 have been replaced by cysteine. The mutants were prepared by cassette mutagenesis of the synthetic bacterio-opsin gene, expression and purification of the mutant apoproteins, renaturation, and chromophore regeneration. The replacement of Trp-10, Trp-12 (helix A), Trp-80 (helix C), and Trp-138 (helix E) by phenylalanine and of Trp-137 and Trp-138 by cysteine did not significantly alter the absorption spectra or affect their proton pumping. However, substitution of the remaining tryptophans by phenylalanine had the following effects. (1) Substitution of Trp-86 (helix C) and Trp-137 gave chromophores blue-shifted by 20 nm and resulted in reduced proton pumping to about 30%. (2) As also reported previously, substitution of Trp-182 and Trp-189 (helix F) caused large blue shifts (70 and 40 nm, respectively) in the chromophore and affected proton pumping. (3) The substitution of Trp-86 and Trp-182 by phenylalanine conferred acid instability on these mutants. The spectral shifts indicate that Trp-86, Trp-182, Trp-189, and possibly Trp-137 interact with retinal. It is proposed that these tryptophans, probably along with Tyr-57 (helix B) and Tyr-185 (helix F), form a retinal binding pocket. We discuss the role of tryptophan residues that are conserved in bacteriorhodopsin, halorhodopsin, and the related family of opsin proteins.

  5. Structure-function studies of the muscle nicotinic acetylcholine receptor by site-directed mutagenesis in the pore region

    NASA Astrophysics Data System (ADS)

    Zhang, Haiyun

    In nicotinic acetylcholine receptors (nAChRs), as in glycine, GABA A, serotonin 5-HT3, and GluCl glutamate receptors, a leucine residue at the approximate midpoint (the 9' position) of the M2 transmembrane domain is conserved across all known subunits. We expressed the embryonic mouse muscle nAChRs with varying numbers (m* s) of subunits (2 αs, 1 β, 1 γ, and 1 δ) mutated at this position in Xenopus oocytes and discovered that mutations to serine (Leu9'Ser) result in a tenfold higher receptor sensitivity to acetylcholine (ACh) for each subunit mutated. Moreover, increases of side-chain polarity increase the sensitivity to ACh when other natural and unnatural residues are incorporated into this position. The data also indicated an especially strong interaction between the γ and δ subunits in the pore region, suggesting a specific arrangement of subunits within the pentamer. Detailed single-channel kinetic studies reveal that Leu9'Ser AChRs have (1) longer voltage- relaxation time constants, (2) longer ACh-induced openings and bursts, and (3) more frequent spontaneous openings. These effects increase with m* s. Synthesized postsynaptic currents were produced with a piezoelectric micromanipulator that delivered brief ACh pulses to multi-channel patches. Their decay time constants were, as expected, similar to the channel burst duration. Thus, both longer and more frequent openings contribute to the >=104-fold increase in the receptor sensitivity to ACh from the wild-type receptor to the receptor with m*s=4; and the highly conserved 9' leucine is crucial for the brief synaptic events that are normally observed. We also explored the effects of ligand-binding domain mutations: γD174N and δD180N (aspartic acid (D) to asparagine (N)). Macroscopic dose-response relations revealed that these mutations decrease the receptor's sensitivity to ACh. The combined effect with Leu9'Ser, however, differs from that predicted from a linear or independent sum of effects from

  6. Defining the Interactions of Cellobiohydrolase with Substrate through Structure Function Studies: Cooperative Research and Development Final Report, CRADA Number CRD-10-409

    SciTech Connect

    Beckham, G. T.; Himmel, M. E.

    2013-07-01

    NREL researchers will use their expertise and skilled resources in numerical computational modeling to generate structure-function relationships for improved cellulase variant enzymes to support the development of cellulases with improved performance in biomass conversion.

  7. Quark-hadron duality in structure functions

    SciTech Connect

    Wally Melnitchouk

    2011-09-01

    We review recent progress in the study of quark-hadron duality in electron–nucleon structure functions. New developments include insights into the local aspects of duality obtained using truncated moments of structure functions, which allow duality-violating higher-twist contributions to be identified in individual resonance regions. Preliminary studies of pion electropro-duction have also showed the first glimpses of duality in semi-inclusive cross sections, which if confirmed would greatly expand the scope of constraining the flavor and spin dependence of parton distributions.

  8. Study of structure-function relationships in proteins: Techniques and applications ot cytochrome c: Final report January 15, 1988--January 14, 1989

    SciTech Connect

    Goldstein, D.A.; Rackovsky, S.R.

    1989-08-01

    During the initial period of this work we explored the differential geometry results which had been used to explain the structure-function relationships in the set of yeast iso-1-cytochrome c mutants studied under the initial contract. In addition we continued the development of techniques which would permit the structural characterization and comparison of proteins in a very efficient manner. We have expanded the studies based on the characterization of the structural preferences of various residues in a sample of twenty six globular proteins. It has been demonstrated that the overall structural preferences and the amino acid specific preferences seen in the analysis carried out at the five alpha carbon level can not be explained by the results of the analysis carried out at the four alpha carbon level. Thus the structural preferences seen must be described by considering groups of five or more residues. We do no yet have enough data to extend the analysis to the six alpha carbon unit level. We have also verified that the yeast/tuna structural analogy which we used before was justified, and have performed a conformational energy minimization of the reduced yeast cytochrome c crystal data in order to have a baseline for the study of mutant proteins. 6 refs.

  9. In Situ and Ex Situ TEM Study of Lithiation Behaviours of Porous Silicon Nanostructures.

    PubMed

    Shen, Chenfei; Ge, Mingyuan; Luo, Langli; Fang, Xin; Liu, Yihang; Zhang, Anyi; Rong, Jiepeng; Wang, Chongmin; Zhou, Chongwu

    2016-01-01

    In this work, we study the lithiation behaviours of both porous silicon (Si) nanoparticles and porous Si nanowires by in situ and ex situ transmission electron microscopy (TEM) and compare them with solid Si nanoparticles and nanowires. The in situ TEM observation reveals that the critical fracture diameter of porous Si particles reaches up to 1.52 μm, which is much larger than the previously reported 150 nm for crystalline Si nanoparticles and 870 nm for amorphous Si nanoparticles. After full lithiation, solid Si nanoparticles and nanowires transform to crystalline Li15Si4 phase while porous Si nanoparticles and nanowires transform to amorphous LixSi phase, which is due to the effect of domain size on the stability of Li15Si4 as revealed by the first-principle molecular dynamic simulation. Ex situ TEM characterization is conducted to further investigate the structural evolution of porous and solid Si nanoparticles during the cycling process, which confirms that the porous Si nanoparticles exhibit better capability to suppress pore evolution than solid Si nanoparticles. The investigation of structural evolution and phase transition of porous Si nanoparticles and nanowires during the lithiation process reveal that they are more desirable as lithium-ion battery anode materials than solid Si nanoparticles and nanowires. PMID:27571919

  10. In Situ and Ex Situ TEM Study of Lithiation Behaviours of Porous Silicon Nanostructures

    PubMed Central

    Shen, Chenfei; Ge, Mingyuan; Luo, Langli; Fang, Xin; Liu, Yihang; Zhang, Anyi; Rong, Jiepeng; Wang, Chongmin; Zhou, Chongwu

    2016-01-01

    In this work, we study the lithiation behaviours of both porous silicon (Si) nanoparticles and porous Si nanowires by in situ and ex situ transmission electron microscopy (TEM) and compare them with solid Si nanoparticles and nanowires. The in situ TEM observation reveals that the critical fracture diameter of porous Si particles reaches up to 1.52 μm, which is much larger than the previously reported 150 nm for crystalline Si nanoparticles and 870 nm for amorphous Si nanoparticles. After full lithiation, solid Si nanoparticles and nanowires transform to crystalline Li15Si4 phase while porous Si nanoparticles and nanowires transform to amorphous LixSi phase, which is due to the effect of domain size on the stability of Li15Si4 as revealed by the first-principle molecular dynamic simulation. Ex situ TEM characterization is conducted to further investigate the structural evolution of porous and solid Si nanoparticles during the cycling process, which confirms that the porous Si nanoparticles exhibit better capability to suppress pore evolution than solid Si nanoparticles. The investigation of structural evolution and phase transition of porous Si nanoparticles and nanowires during the lithiation process reveal that they are more desirable as lithium-ion battery anode materials than solid Si nanoparticles and nanowires. PMID:27571919

  11. Chemical Library Screening and Structure-Function Relationship Studies Identify Bisacodyl as a Potent and Selective Cytotoxic Agent Towards Quiescent Human Glioblastoma Tumor Stem-Like Cells

    PubMed Central

    Mameri, Samir; Dong, Jihu; Salomé, Christophe; Chen, Wanyin; El-Habr, Elias A.; Bousson, Fanny; Sy, Mohamadou; Obszynski, Julie; Boh, Alexandre; Villa, Pascal; Assad Kahn, Suzana; Didier, Bruno; Bagnard, Dominique; Junier, Marie-Pierre; Chneiweiss, Hervé; Haiech, Jacques; Hibert, Marcel; Kilhoffer, Marie-Claude

    2015-01-01

    Cancer stem-like cells reside in hypoxic and slightly acidic tumor niches. Such microenvironments favor more aggressive undifferentiated phenotypes and a slow growing "quiescent state" which preserves them from chemotherapeutic agents that essentially target proliferating cells. Our objective was to identify compounds active on glioblastoma stem-like cells, including under conditions that mimick those found in vivo within this most severe and incurable form of brain malignancy. We screened the Prestwick Library to identify cytotoxic compounds towards glioblastoma stem-like cells, either in a proliferating state or in more slow-growing "quiescent" phenotype resulting from non-renewal of the culture medium in vitro. Compound effects were assessed by ATP-level determination using a cell-based assay. Twenty active molecules belonging to different pharmacological classes have thus been identified. Among those, the stimulant laxative drug bisacodyl was the sole to inhibit in a potent and specific manner the survival of quiescent glioblastoma stem-like cells. Subsequent structure-function relationship studies led to identification of 4,4'-dihydroxydiphenyl-2-pyridyl-methane (DDPM), the deacetylated form of bisacodyl, as the pharmacophore. To our knowledge, bisacodyl is currently the only known compound targeting glioblastoma cancer stem-like cells in their quiescent, more resistant state. Due to its known non-toxicity in humans, bisacodyl appears as a new potential anti-tumor agent that may, in association with classical chemotherapeutic compounds, participate in tumor eradication. PMID:26270679

  12. Total synthesis of vinblastine, related natural products, and key analogues and development of inspired methodology suitable for the systematic study of their structure-function properties.

    PubMed

    Sears, Justin E; Boger, Dale L

    2015-03-17

    Biologically active natural products composed of fascinatingly complex structures are often regarded as not amenable to traditional systematic structure-function studies enlisted in medicinal chemistry for the optimization of their properties beyond what might be accomplished by semisynthetic modification. Herein, we summarize our recent studies on the Vinca alkaloids vinblastine and vincristine, often considered as prototypical members of such natural products, that not only inspired the development of powerful new synthetic methodology designed to expedite their total synthesis but have subsequently led to the discovery of several distinct classes of new, more potent, and previously inaccessible analogues. With use of the newly developed methodology and in addition to ongoing efforts to systematically define the importance of each embedded structural feature of vinblastine, two classes of analogues already have been discovered that enhance the potency of the natural products >10-fold. In one instance, remarkable progress has also been made on the refractory problem of reducing Pgp transport responsible for clinical resistance with a series of derivatives made accessible only using the newly developed synthetic methodology. Unlike the removal of vinblastine structural features or substituents, which typically has a detrimental impact, the additions of new structural features have been found that can enhance target tubulin binding affinity and functional activity while simultaneously disrupting Pgp binding, transport, and functional resistance. Already analogues are in hand that are deserving of full preclinical development, and it is a tribute to the advances in organic synthesis that they are readily accessible even on a natural product of a complexity once thought refractory to such an approach. PMID:25586069

  13. Progress on nuclear modifications of structure functions

    NASA Astrophysics Data System (ADS)

    Kumano, S.

    2016-03-01

    We report progress on nuclear structure functions, especially on their nuclear modifications and a new tensor structure function for the deuteron. To understand nuclear structure functions is an important step toward describing nuclei and QCD matters from low to high densities and from low to high energies in terms of fundamental quark and gluon degrees of freedom beyond conventional hadron and nuclear physics. It is also practically important for understanding new phenomena in high-energy heavy-ion collisions at RHIC and LHC. Furthermore, since systematic errors of current neutrinooscillation experiments are dominated by uncertainties of neutrino-nucleus interactions, such studies are valuable for finding new physics beyond current framework. Next, a new tensor-polarized structure function b1 is discussed for the deuteron. There was a measurement by HERMES; however, its data are inconsistent with the conventional convolution estimate based on the standard deuteron model with D-state admixture. This fact suggests that a new hadronic phenomenon should exist in the tensor-polarized deuteron at high energies, and it will be experimentally investigated at JLab from the end of 2010's.

  14. Structure functions and parton distributions

    SciTech Connect

    Martin, A.D.; Stirling, W.J.; Roberts, R.G.

    1995-07-01

    The MRS parton distribution analysis is described. The latest sets are shown to give an excellent description of a wide range of deep-inelastic and other hard scattering data. Two important theoretical issues-the behavior of the distributions at small x and the flavor structure of the quark sea-are discussed in detail. A comparison with the new structure function data from HERA is made, and the outlook for the future is discussed.

  15. Truncated Moment Analysis of Nucleon Structure Functions

    SciTech Connect

    A. Psaker; W. Melnitchouk; M. E. Christy; C. E. Keppel

    2007-11-16

    We employ a novel new approach using "truncated" moments, or integrals of structure functions over restricted regions of x, to study local quark-hadron duality, and the degree to which individual resonance regions are dominated by leading twists. Because truncated moments obey the same Q^2 evolution equations as the leading twist parton distributions, this approach makes possible for the first time a description of resonance region data and the phenomenon of quark-hadron duality directly from QCD.

  16. The Design, Synthesis, and Study of Solid-State Molecular Rotors: Structure/Function Relationships for Condensed-Phase Anisotropic Dynamics

    NASA Astrophysics Data System (ADS)

    Vogelsberg, Cortnie Sue

    Amphidynamic crystals are an extremely promising platform for the development of artificial molecular machines and stimuli-responsive materials. In analogy to skeletal muscle, their function will rely upon the collective operation of many densely packed molecular machines (i.e. actin-bound myosin) that are self-assembled in a highly organized anisotropic medium. By choosing lattice-forming elements and moving "parts" with specific functionalities, individual molecular machines may be synthesized and self-assembled in order to carry out desirable functions. In recent years, efforts in the design of amphidynamic materials based on molecular gyroscopes and compasses have shown that a certain amount of free volume is essential to facilitate internal rotation and reorientation within a crystal. In order to further establish structure/function relationships to advance the development of increasingly complex molecular machinery, molecular rotors and a molecular "spinning" top were synthesized and incorporated into a variety of solid-state architectures with different degrees of periodicity, dimensionality, and free volume. Specifically, lamellar molecular crystals, hierarchically ordered periodic mesoporous organosilicas, and metal-organic frameworks were targeted for the development of solid-state molecular machines. Using an array of solid-state nuclear magnetic resonance spectroscopy techniques, the dynamic properties of these novel molecular machine assemblies were determined and correlated with their corresponding structural features. It was found that architecture type has a profound influence on functional dynamics. The study of layered molecular crystals, composed of either molecular rotors or "spinning" tops, probed functional dynamics within dense, highly organized environments. From their study, it was discovered that: 1) crystallographically distinct sites may be utilized to differentiate machine function, 2) halogen bonding interactions are sufficiently

  17. Structure functions for light nuclei

    SciTech Connect

    S.A. Kulagin, R. Petti

    2010-11-01

    We discuss the nuclear EMC effect with particular emphasis on recent data for light nuclei including 2H, 3He, 4He, 9Be, 12C and 14N. In order to verify the consistency of available data, we calculate the \\chi^2 deviation between different data sets. We find a good agreement between the results from the NMC, SLAC E139, and HERMES experiments. However, our analysis indicates an overall normalization offset of about 2% in the data from the recent JLab E03-103 experiment with respect to previous data for nuclei heavier than 3He. We also discuss the extraction of the neutron/proton structure function ratio F2n/F2p from the nuclear ratios 3He/2H and 2H/1H. Our analysis shows that the E03-103 data on 3He/2H require a renormalization of about 3% in order to be consistent with the F2n/F2p ratio obtained from the NMC experiment. After such a renormalization, the 3He data from the E03-103 data and HERMES experiments are in a good agreement. Finally, we present a detailed comparison between data and model calculations, which include a description of the nuclear binding, Fermi motion and off-shell corrections to the structure functions of bound proton and neutron, as well as the nuclear pion and shadowing corrections. Overall, a good agreement with the available data for all nuclei is obtained.

  18. Nuclear structure functions at small x

    SciTech Connect

    Jalilian-Marian, Jamal

    2009-11-15

    I study the nuclear structure function F{sub 2}{sup A} and its logarithmic derivative in the high-energy limit (small-x region) using the color glass condensate formalism. In this limit the structure function F{sub 2} depends on the quark-antiquark dipole-target scattering cross section N{sub F}(x{sub bj},r{sub t},b{sub t}). The same dipole cross section appears in single-hadron and hadron-photon production cross sections in the forward rapidity region in deuteron (proton)-nucleus collisions at high energy, that is, at energies available at the BNL Relativistic Heavy Ion Collider (RHIC) and the CERN Large Hadron Collider (LHC). I use a parametrization of the dipole cross section, which has successfully been used to describe the deuteron-gold data at the RHIC, to compute the nuclear structure function F{sub 2}{sup A} and its log Q{sup 2} derivative (which is related to gluon distribution function in the double log limit). I provide a quantitative estimate of the nuclear shadowing of F{sub 2}{sup A} and the gluon distribution function in the kinematic region relevant to a future electron-ion collider.

  19. Underwater microscopy for in situ studies of benthic ecosystems

    PubMed Central

    Mullen, Andrew D.; Treibitz, Tali; Roberts, Paul L. D.; Kelly, Emily L. A.; Horwitz, Rael; Smith, Jennifer E.; Jaffe, Jules S.

    2016-01-01

    Microscopic-scale processes significantly influence benthic marine ecosystems such as coral reefs and kelp forests. Due to the ocean's complex and dynamic nature, it is most informative to study these processes in the natural environment yet it is inherently difficult. Here we present a system capable of non-invasively imaging seafloor environments and organisms in situ at nearly micrometre resolution. We overcome the challenges of underwater microscopy through the use of a long working distance microscopic objective, an electrically tunable lens and focused reflectance illumination. The diver-deployed instrument permits studies of both spatial and temporal processes such as the algal colonization and overgrowth of bleaching corals, as well as coral polyp behaviour and interspecific competition. By enabling in situ observations at previously unattainable scales, this instrument can provide important new insights into micro-scale processes in benthic ecosystems that shape observed patterns at much larger scales. PMID:27403715

  20. Underwater microscopy for in situ studies of benthic ecosystems

    NASA Astrophysics Data System (ADS)

    Mullen, Andrew D.; Treibitz, Tali; Roberts, Paul L. D.; Kelly, Emily L. A.; Horwitz, Rael; Smith, Jennifer E.; Jaffe, Jules S.

    2016-07-01

    Microscopic-scale processes significantly influence benthic marine ecosystems such as coral reefs and kelp forests. Due to the ocean's complex and dynamic nature, it is most informative to study these processes in the natural environment yet it is inherently difficult. Here we present a system capable of non-invasively imaging seafloor environments and organisms in situ at nearly micrometre resolution. We overcome the challenges of underwater microscopy through the use of a long working distance microscopic objective, an electrically tunable lens and focused reflectance illumination. The diver-deployed instrument permits studies of both spatial and temporal processes such as the algal colonization and overgrowth of bleaching corals, as well as coral polyp behaviour and interspecific competition. By enabling in situ observations at previously unattainable scales, this instrument can provide important new insights into micro-scale processes in benthic ecosystems that shape observed patterns at much larger scales.

  1. Underwater microscopy for in situ studies of benthic ecosystems.

    PubMed

    Mullen, Andrew D; Treibitz, Tali; Roberts, Paul L D; Kelly, Emily L A; Horwitz, Rael; Smith, Jennifer E; Jaffe, Jules S

    2016-01-01

    Microscopic-scale processes significantly influence benthic marine ecosystems such as coral reefs and kelp forests. Due to the ocean's complex and dynamic nature, it is most informative to study these processes in the natural environment yet it is inherently difficult. Here we present a system capable of non-invasively imaging seafloor environments and organisms in situ at nearly micrometre resolution. We overcome the challenges of underwater microscopy through the use of a long working distance microscopic objective, an electrically tunable lens and focused reflectance illumination. The diver-deployed instrument permits studies of both spatial and temporal processes such as the algal colonization and overgrowth of bleaching corals, as well as coral polyp behaviour and interspecific competition. By enabling in situ observations at previously unattainable scales, this instrument can provide important new insights into micro-scale processes in benthic ecosystems that shape observed patterns at much larger scales. PMID:27403715

  2. Structure functions for light nuclei

    SciTech Connect

    Kulagin, S. A.; Petti, R.

    2010-11-15

    We discuss the nuclear EMC effect with particular emphasis on recent data for light nuclei including {sup 2}H, {sup 3}He, {sup 4}He, {sup 9}Be, {sup 12}C, and {sup 14}N. In order to verify the consistency of available data, we calculate the {chi}{sup 2} deviation between different data sets. We find a good agreement between the results from the NMC, SLAC E139, and HERMES experiments. However, our analysis indicates an overall normalization offset of about 2% in the data from the recent JLab E03-103 experiment with respect to previous data for nuclei heavier than {sup 3}He. We also discuss the extraction of the neutron/proton structure function ratio F{sub 2}{sup n}/F{sub 2}{sup p} from the nuclear ratios {sup 3}He/{sup 2}H and {sup 2}H/{sup 1}H. Our analysis shows that the E03-103 data on {sup 3}He/{sup 2}H require a renormalization of about 3% in order to be consistent with the F{sub 2}{sup n}/F{sub 2}{sup p} ratio obtained from the NMC experiment. After such a renormalization, the {sup 3}He data from the E03-103 and HERMES experiments are in a good agreement. Finally, we present a detailed comparison between data and model calculations, which include a description of the nuclear binding, Fermi motion, and off-shell corrections to the structure functions of bound proton and neutron, as well as the nuclear pion and shadowing corrections. Overall, a good agreement with the available data for all nuclei is obtained.

  3. Indentation device for in situ Raman spectroscopic and optical studies

    NASA Astrophysics Data System (ADS)

    Gerbig, Y. B.; Michaels, C. A.; Forster, A. M.; Hettenhouser, J. W.; Byrd, W. E.; Morris, D. J.; Cook, R. F.

    2012-12-01

    Instrumented indentation is a widely used technique to study the mechanical behavior of materials at small length scales. Mechanical tests of bulk materials, microscopic, and spectroscopic studies may be conducted to complement indentation and enable the determination of the kinetics and physics involved in the mechanical deformation of materials at the crystallographic and molecular level, e.g., strain build-up in crystal lattices, phase transformations, and changes in crystallinity or orientation. However, many of these phenomena occurring during indentation can only be observed in their entirety and analyzed in depth under in situ conditions. This paper describes the design, calibration, and operation of an indentation device that is coupled with a Raman microscope to conduct in situ spectroscopic and optical analysis of mechanically deformed regions of Raman-active, transparent bulk material, thin films or fibers under contact loading. The capabilities of the presented device are demonstrated by in situ studies of the indentation-induced phase transformations of Si thin films and modifications of molecular conformations in high density polyethylene films.

  4. Calcite dissolution: an in situ study in the Panama Basin

    SciTech Connect

    Thunell, R.C.; Keir, R.S.; Honjo, S.

    1981-05-08

    The results of an in situ study of calcite dissolution in the Panama Basin indicate that the rate of dissolution in the water column increases suddenly below a water depth of about 2800 meters. This coincides with the depth at which the calcium carbonate content of surface sediments begins to decrease rapidly or the sedimentary lysocline. Since this level of increased dissolution both in the water column and on the sea floor does not appear to be related to the transition from supersaturation to undersaturation with respect to carbonate, there may be a kinetic origin for the lysocline in this region.

  5. In situ studies of grain growth in thin metal films

    SciTech Connect

    Nichols, C.S.; Mansuri, C.M. . Dept. of Materials Science and Engineering); Townsend, S.J. . Dept. of Physics); Smith, D.A. . T.J. Watson Research Center)

    1993-06-01

    Grain growth in thin films of aluminum has been studied using in situ transmission electron microscopy and a heating stage. Videotapes taken during grain growth were analyzed with the intent of searching for the predominant local rearrangement processes responsible for growth. Evolution of a soap froth can be decomposed into only two elementary local topology rearranging events. The authors have found numerous exceptions to prevailing theories that compare grain growth in thin films to the evolution of such froths. These observations suggest that a more complete picture of grain growth is necessary and that such a theory must include more complex local rearrangement processes.

  6. Spin Structure Function Measurements in Hall C at Jefferson Lab

    SciTech Connect

    Wood, Stephen A.

    2008-11-01

    This presentation introduces the spin structure functions and resonant spin structure, and it discusses the experimental approaches for studying spin structure via polarized electron beam interactions with frozen polarized proton and deuteron targets.

  7. In situ TEM studies of carbon and gold nanostructures

    NASA Astrophysics Data System (ADS)

    Casillas Garcia, Gilberto

    Properties of matter change as structures go down in size to the nanoscale, creating new possibilities for creating new functional materials with better properties than the bulk. In situ TEM techniques were used to probe the properties of two different materials: atomic carbon chains and gold nanoparticles. Carbon chains were synthesized by in situ TEM electron beam irradiation from few-layers-graphene (FLG) flakes. Several chains up to 5 nm long were observed. Aberration corrected TEM confirmed the dimerization of the linear chain as predicted by Peierls. Moreover, it was observed that two linear carbon chains can cross-bond every 9 atoms, and it was confirmed by DFT calculations. Five-fold nanoparticles are not supposed to be stable beyond 5 nm size. Here, decahedra with high index facets in the order of 300 nm were studied by TEM. It was found that the high index facets were only stable by adding a capping agent, otherwise, smooth edges were observed. In this case, a (5x1) hexagonal surface reconstruction was observed on the {001} surfaces, with the hexagonal strings along a [110] and a [410] direction. Additionally, mechanical properties of gold nanoparticles, with and without twin boundaries, under 100 nm were measured by in situ TEM compression experiments. All of the nanoparticles presented yield strengths in the order of GPa. Multi twinned nanoparticles were found to be more malleable, reaching real compressing strains of 100 %, while the single crystal nanoparticle presented less plastic flow. Molecular dynamics simulations revealed that the twin boundaries contribute to the malleability of the nanoparticles, at the same time it provides a mechanism to stop dislocations, hence, strain hardening the nanoparticle at later stages of compression. Finally, the behavior of a single grain boundary was studied by in situ TEM manipulation of nanoparticles. A liquid-like behavior of a grain boundary is observed after two 40 nm gold nanoparticles are brought to

  8. Integral structural-functional method for characterizing microbial populations

    NASA Astrophysics Data System (ADS)

    Yakushev, A. V.

    2015-04-01

    An original integral structural-functional method has been proposed for characterizing microbial communities. The novelty of the approach is the in situ study of microorganisms based on the growth kinetics of microbial associations in liquid nutrient broth media under selective conditions rather than on the level of taxa or large functional groups. The method involves the analysis of the integral growth model of a periodic culture. The kinetic parameters of such associations reflect their capacity of growing on different media, i.e., their physiological diversity, and the metabolic capacity of the microorganisms for growth on a nutrient medium. Therefore, the obtained parameters are determined by the features of the microbial ecological strategies. The inoculation of a dense medium from the original inoculate allows characterizing the taxonomic composition of the dominants in the soil community. The inoculation from the associations developed on selective media characterizes the composition of syntrophic groups, which fulfill a specific function in nature. This method is of greater information value than the classical methods of inoculation on selective media.

  9. Guanylyl cyclase structure, function and regulation

    PubMed Central

    Potter, Lincoln R.

    2016-01-01

    Nitric oxide, bicarbonate, natriuretic peptides (ANP, BNP and CNP), guanylins, uroguanylins and guanylyl cyclase activating proteins (GCAPs) activate a family of enzymes variously called guanyl, guanylyl or guanylate cyclases that catalyze the conversion of guanosine triphosphate to cyclic guanosine monophosphate (cGMP) and pyrophosphate. Intracellular cyclic GMP is a second messenger that modulates: platelet aggregation, neurotransmission, sexual arousal, gut peristalsis, blood pressure, long bone growth, intestinal fluid secretion, lipolysis, phototransduction, cardiac hypertrophy and oocyte maturation. This review briefly discusses the discovery of cGMP and guanylyl cyclases, then nitric oxide, nitric oxide synthase and soluble guanylyl cyclase are described in slightly greater detail. Finally, the structure, function, and regulation of the individual mammalian single membrane-spanning guanylyl cyclases GC-A, GC-B, GC-C, GC-D, GC-E, GC-F and GC-G are described in greatest detail as determined by biochemical, cell biological and gene-deletion studies. PMID:21914472

  10. Intraductal Therapy of Ductal Carcinoma In Situ: A Presurgery Study

    PubMed Central

    Mahoney, M. Ellen; Gordon, Eva J.; Rao, Jian Yu; Jin, Yusheng; Hylton, Nola; Love, Susan M.

    2014-01-01

    Many women with ductal carcinoma in situ (DCIS) are treated with extensive surgery, radiation, and hormone therapy due to the inability to monitor the disease and to determine which cases will progress to invasive cancer. We assessed the safety and feasibility of administering chemotherapy directly into DCIS-containing ducts in 13 women before definitive surgery. The treatment was safe, feasible, and well tolerated, supporting further development of this strategy for management of DCIS. Introduction Ductal carcinoma in situ (DCIS) is a noninvasive breast cancer wherein malignant cells are confined within a ductal lobular unit. Although less than half the cases of DCIS will progress to invasive disease, most women are treated aggressively with surgery, radiation, and/or hormone therapy due to the inability to clinically evaluate the extent and location of the disease. Intraductal therapy, in which a drug is administered directly into the mammary duct through the nipple, is a promising approach for treating DCIS, but the feasibility of instilling drug into a diseased duct has not been established. Patients and Methods Four to 6 weeks before their scheduled surgery, 13 women diagnosed with DCIS were subjected to cannulation of the affected duct. After both the absence of perforation and presence of dye in the duct were confirmed by ductogram, pegylated liposomal doxorubicin was instilled. Histopathologic assessment was performed after surgery to assess the treatment effects. Results Of the 13 women enrolled in the study, 6 had their DCIS duct successfully cannulated without perforation and instilled with the drug. The treatment was well tolerated, and no serious adverse events have been reported. Biomarker studies indicated a general decrease in Ki-67 levels but an increase in annexin-1 and 8-hydroxydeoxyguanosine in the lumen of DCIS-containing ducts, which suggests a local response to pegylated liposomal doxorubicin treatment. Conclusions Intraductal therapy offers

  11. Mass Effects on the Nucleon Sea Structure Functions

    NASA Astrophysics Data System (ADS)

    Kim, Sun Myong

    Nucleon sea structure functions are studied using Dokshitzer-Gribov-Lipatov-Altarelli-Parisi (DGLAP) equations with the massive gluon-quark splitting kernels for strange and charm quarks, the massless gluon-quark splitting kernels for up and down quarks, and the massless kernels for all other splitting parts. The SU(2)f flavor symmetry for two light quarks, ``up'' and ``down'', is assumed. Glück-Reya-Vogt (GRV) and Martin-Roberts-Stirling (MRS) sets are chosen to be the base structure functions at Q02=3 GeV2. We evolve the sea structure functions from Q02=3 GeV2 to Q2=50 GeV2 using the base structure function sets and DGLAP equations. Some (about 10%) enhancement is found in the strange quark distribution functions at low x (<0.1) in leading order of the DGLAP equations compared to results directly from those structure function sets at the value of Q2=50 GeV2. We provide the value of κ and also show the behavior of κ (x)=2s(x)/(¯ u(x)+¯ d(x)) after the evolution of structure functions.

  12. Structured Functional Principal Component Analysis

    PubMed Central

    Shou, Haochang; Zipunnikov, Vadim; Crainiceanu, Ciprian M.; Greven, Sonja

    2015-01-01

    Summary Motivated by modern observational studies, we introduce a class of functional models that expand nested and crossed designs. These models account for the natural inheritance of the correlation structures from sampling designs in studies where the fundamental unit is a function or image. Inference is based on functional quadratics and their relationship with the underlying covariance structure of the latent processes. A computationally fast and scalable estimation procedure is developed for high-dimensional data. Methods are used in applications including high-frequency accelerometer data for daily activity, pitch linguistic data for phonetic analysis, and EEG data for studying electrical brain activity during sleep. PMID:25327216

  13. Structured functional principal component analysis.

    PubMed

    Shou, Haochang; Zipunnikov, Vadim; Crainiceanu, Ciprian M; Greven, Sonja

    2015-03-01

    Motivated by modern observational studies, we introduce a class of functional models that expand nested and crossed designs. These models account for the natural inheritance of the correlation structures from sampling designs in studies where the fundamental unit is a function or image. Inference is based on functional quadratics and their relationship with the underlying covariance structure of the latent processes. A computationally fast and scalable estimation procedure is developed for high-dimensional data. Methods are used in applications including high-frequency accelerometer data for daily activity, pitch linguistic data for phonetic analysis, and EEG data for studying electrical brain activity during sleep. PMID:25327216

  14. Mechanistic studies of malonic acid-mediated in situ acylation.

    PubMed

    Chandra, Koushik; Naoum, Johnny N; Roy, Tapta Kanchan; Gilon, Chaim; Gerber, R Benny; Friedler, Assaf

    2015-09-01

    We have previously introduced an easy to perform, cost-effective and highly efficient acetylation technique for solid phase synthesis (SPPS). Malonic acid is used as a precursor and the reaction proceeds via a reactive ketene that acetylates the target amine. Here we present a detailed mechanistic study of the malonic acid-mediated acylation. The influence of reaction conditions, peptide sequence and reagents was systematically studied. Our results show that the methodology can be successfully applied to different types of peptides and nonpeptidic molecules irrespective of their structure, sequence, or conformation. Using alkyl, phenyl, and benzyl malonic acid, we synthesized various acyl peptides with almost quantitative yields. The ketenes obtained from the different malonic acid derived precursors were characterized by in situ (1) H-NMR. The reaction proceeded in short reaction times and resulted in excellent yields when using uronium-based coupling agents, DIPEA as a base, DMF/DMSO/NMP as solvents, Rink amide/Wang/Merrifield resins, temperature of 20°C, pH 8-12 and 5 min preactivation at inert atmosphere. The reaction was unaffected by Lewis acids, transition metal ions, surfactants, or salt. DFT studies support the kinetically favorable concerted mechanism for CO2 and ketene formation that leads to the thermodynamically stable acylated products. We conclude that the malonic acid-mediated acylation is a general method applicable to various target molecules. PMID:25846609

  15. RANGELAND COMMUNITIES: STRUCTURE, FUNCTION, AND CLASSIFICATION

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Determining the vegetational attributes of rangelands is critical to their management. Yet incorporating vegetation structure, function, and classification into a single chapter is an ambitious goal and an attempt to blur the boundaries between classical community ecology that characterize patterns...

  16. Microbial Studies Supporting Implementation of In Situ Bioremediation at TAN

    SciTech Connect

    Barnes, Joan Marie; Matthern, Gretchen Elise; Rae, Catherine; Ely, R. L.

    2000-11-01

    The Idaho National Engineering and Environmental Laboratory is evaluating in situ bioremediation of contaminated groundwater at its Test Area North Facility. To determine feasibility, microcosm and bioreactor studies were conducted to ascertain the ability of indigenous microbes to convert trichloroethene and dichloroethene to non-hazardous byproducts under aerobic and anaerobic conditions, and to measure the kinetics of microbial reactions associated with the degradation process. Microcosms were established from core samples and groundwater obtained from within the contaminant plume. These microcosms were amended with nutrients, under aerobic and anaerobic conditions, to identify electron donors capable of stimulating the degradation process. Results of the anaerobic microcosm studies showed that lactate, acetate and propionate amendments stimulated indigenous cell growth and functioned as effective substrates for reductive degradation of chloroethenes. Bioreactors inoculated with cultures from these anaerobic microcosms were operated under a batch mode for 42 days then converted to a fed-batch mode and operated at a 53-day hydraulic residence time. It was demonstrated that indigenous microbes capable of complete anaerobic reductive dechlorination are present in the subject well. It was also demonstrated that aerobic microbes capable of oxidizing chlorinated compounds produced by anaerobic reductive dechlorination are present. Kinetic data suggest that controlling the type and concentration of electron donors can increase trichlorethene conversion rates. In the event that complete mineralization of trichlorethene does not occur following stimulation, and anaerobic/aerobic treatment scheme is feasible.

  17. Process-Structure-Function Relations of Pectin in Food.

    PubMed

    Christiaens, Stefanie; Van Buggenhout, Sandy; Houben, Ken; Jamsazzadeh Kermani, Zahra; Moelants, Katlijn R N; Ngouémazong, Eugénie D; Van Loey, Ann; Hendrickx, Marc E G

    2016-04-25

    Pectin, a complex polysaccharide rich in galacturonic acid, has been identified as a critical structural component of plant cell walls. The functionality of this intricate macromolecule in fruit- and vegetable-based-derived products and ingredients is strongly determined by the nanostructure of its most abundant polymer, homogalacturonan. During food processing, pectic homogalacturonan is susceptible to various enzymatic as well as nonenzymatic conversion reactions modifying its structural and, hence, its functional properties. Consequently, a profound understanding of the various process-structure-function relations of pectin aids food scientists to tailor the functional properties of plant-based derived products and ingredients. This review describes the current knowledge on process-structure-function relations of pectin in foods with special focus on pectin's functionality with regard to textural attributes of solid plant-based foods and rheological properties of particulated fruit- and vegetable-derived products. In this context, both pectin research performed via traditional, ex situ physicochemical analyses of fractionated walls and isolated polymers and pectin investigation through in situ pectin localization are considered. PMID:25629167

  18. Generation of recombinant monoclonal antibodies to study structure-function of envelope protein VP28 of white spot syndrome virus from shrimp

    SciTech Connect

    Wang Yuzhen; Zhang Xiaohua; Yuan Li; Xu Tao; Rao Yu; Li Jia; Dai Heping

    2008-08-08

    White spot syndrome virus (WSSV) is a major pathogen in shrimp aquaculture. VP28 is one of the most important envelope proteins of WSSV. In this study, a recombinant antibody library, as single-chain fragment variable (scFv) format, displayed on phage was constructed using mRNA from spleen cells of mice immunized with full-length VP28 expressed in Escherichia coli. After several rounds of panning, six scFv antibodies specifically binding to the epitopes in the N-terminal, middle, and C-terminal regions of VP28, respectively, were isolated from the library. Using these scFv antibodies as tools, the epitopes in VP28 were located on the envelope of the virion by immuno-electron microscopy. Neutralization assay with these antibodies in vitro suggested that these epitopes may not be the attachment site of WSSV to host cell receptor. This study provides a new way to investigate the structure and function of the envelope proteins of WSSV.

  19. Circovirus-infected geese studied by in situ hybridization.

    PubMed

    Smyth, Joan; Soike, D; Moffett, Deborah; Weston, J H; Todd, D

    2005-06-01

    It has now been established that circovirus infection is common in farmed geese, but little is known about the clinicopathological significance of such infections. Ten clinically diseased geese suspected of being infected by circovirus were studied by in situ hybridization using a goose circovirus DNA probe. Circovirus DNA was demonstrated in the bursa of Fabricius (BF), spleen, thymus, bone marrow, liver, kidney, lung and heart, indicating that infection can be multisystemic. In some birds, virus DNA was present in very large quantities, most notably in the BF, liver and small intestine. With the exception of BF and thymus, there were no histological findings that would have suggested the presence of such quantities of circovirus DNA. In view of the very large quantities of virus DNA labelling present in some tissues, and by analogy to porcine circovirus type 2 infection and psittacine beak and feather virus infections, which are known to cause severe disease, and which have similar virus distribution to that found in our geese, it seems probable that the circovirus was important in the disease manifestations shown by the infected geese. PMID:16191706

  20. Structure-Function Studies of Naphthalene, Phenanthrene, Biphenyl, and Their Derivatives in Interaction with and Oxidation by Cytochromes P450 2A13 and 2A6.

    PubMed

    Shimada, Tsutomu; Takenaka, Shigeo; Kakimoto, Kensaku; Murayama, Norie; Lim, Young-Ran; Kim, Donghak; Foroozesh, Maryam K; Yamazaki, Hiroshi; Guengerich, F Peter; Komori, Masayuki

    2016-06-20

    Naphthalene, phenanthrene, biphenyl, and their derivatives having different ethynyl, propynyl, butynyl, and propargyl ether substitutions were examined for their interaction with and oxidation by cytochromes P450 (P450) 2A13 and 2A6. Spectral interaction studies suggested that most of these chemicals interacted with P450 2A13 to induce Type I binding spectra more readily than with P450 2A6. Among the various substituted derivatives examined, 2-ethynylnaphthalene, 2-naphthalene propargyl ether, 3-ethynylphenanthrene, and 4-biphenyl propargyl ether had larger ΔAmax/Ks values in inducing Type I binding spectra with P450 2A13 than their parent compounds. P450 2A13 was found to oxidize naphthalene, phenanthrene, and biphenyl to 1-naphthol, 9-hydroxyphenanthrene, and 2- and/or 4-hydroxybiphenyl, respectively, at much higher rates than P450 2A6. Other human P450 enzymes including P450s 1A1, 1A2, 1B1, 2C9, and 3A4 had lower rates of oxidation of naphthalene, phenanthrene, and biphenyl than P450s 2A13 and 2A6. Those alkynylated derivatives that strongly induced Type I binding spectra with P450s 2A13 and 2A6 were extensively oxidized by these enzymes upon analysis with HPLC. Molecular docking studies supported the hypothesis that ligand-interaction energies (U values) obtained with reported crystal structures of P450 2A13 and 2A6 bound to 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone, indole, pilocarpine, nicotine, and coumarin are of use in understanding the basis of possible molecular interactions of these xenobiotic chemicals with the active sites of P450 2A13 and 2A6 enzymes. In fact, the ligand-interaction energies with P450 2A13 4EJG bound to these chemicals were found to relate to their induction of Type I binding spectra. PMID:27137136

  1. The odyssey of a young gene: structure-function studies in human glutamate dehydrogenases reveal evolutionary-acquired complex allosteric regulation mechanisms.

    PubMed

    Zaganas, Ioannis V; Kanavouras, Konstantinos; Borompokas, Nikolas; Arianoglou, Giovanna; Dimovasili, Christina; Latsoudis, Helen; Vlassi, Metaxia; Mastorodemos, Vasileios

    2014-01-01

    Mammalian glutamate dehydrogenase (GDH) catalyzes the reversible inter-conversion of glutamate to α-ketoglutarate and ammonia, interconnecting carbon skeleton and nitrogen metabolism. In addition, it functions as an energy switch by its ability to fuel the Krebs cycle depending on the energy status of the cell. As GDH lies at the intersection of several metabolic pathways, its activity is tightly regulated by several allosteric compounds that are metabolic intermediates. In contrast to other mammals that have a single GDH-encoding gene, humans and great apes possess two isoforms of GDH (hGDH1 and hGDH2, encoded by the GLUD1 and GLUD2 genes, respectively) with distinct regulation pattern, but remarkable sequence similarity (they differ, in their mature form, in only 15 of their 505 amino-acids). The GLUD2 gene is considered a very young gene, emerging from the GLUD1 gene through retro-position only recently (<23 million years ago). The new hGDH2 iso-enzyme, through random mutations and natural selection, is thought to have conferred an evolutionary advantage that helped its persistence through primate evolution. The properties of the two highly homologous human GDHs have been studied using purified recombinant hGDH1 and hGDH2 proteins obtained by expression of the corresponding cDNAs in Sf21 cells. According to these studies, in contrast to hGDH1 that maintains basal activity at 35-40 % of its maximal, hGDH2 displays low basal activity that is highly responsive to activation by rising levels of ADP and/or L-leucine which can also act synergistically. While hGDH1 is inhibited potently by GTP, hGDH2 shows remarkable GTP resistance. Furthermore, the two iso-enzymes are differentially inhibited by estrogens, polyamines and neuroleptics, and also differ in heat-lability. To elucidate the molecular mechanisms that underlie these different regulation patterns of the two iso-enzymes (and consequently the evolutionary adaptation of hGDH2 to a new functional role), we have

  2. Structure/Function Studies Involving the V3 Region of the HIV-1 Envelope Delineate Multiple Factors That Affect Neutralization Sensitivity

    PubMed Central

    Cohen, Sandra Sharpe; Boyd, David; Kong, Xiang-Peng; Seaman, Michael; Nussenzweig, Michel; Klein, Florian; Overbaugh, Julie; Totrov, Max

    2015-01-01

    ABSTRACT Antibodies (Abs) specific for the V3 loop of the HIV-1 gp120 envelope neutralize most tier 1 and many tier 2 viruses and are present in essentially all HIV-infected individuals as well as immunized humans and animals. Vaccine-induced V3 Abs are associated with reduced HIV infection rates in humans and affect the nature of transmitted viruses in infected vaccinees, despite the fact that V3 is often occluded in the envelope trimer. Here, we link structural and experimental data showing how conformational alterations of the envelope trimer render viruses exceptionally sensitive to V3 Abs. The experiments interrogated the neutralization sensitivity of pseudoviruses with single amino acid mutations in various regions of gp120 that were predicted to alter packing of the V3 loop in the Env trimer. The results indicate that the V3 loop is metastable in the envelope trimer on the virion surface, flickering between states in which V3 is either occluded or available for binding to chemokine receptors (leading to infection) and to V3 Abs (leading to virus neutralization). The spring-loaded V3 in the envelope trimer is easily released by disruption of the stability of the V3 pocket in the unliganded trimer or disruption of favorable V3/pocket interactions. Formation of the V3 pocket requires appropriate positioning of the V1V2 domain, which is, in turn, dependent on the conformation of the bridging sheet and on the stability of the V1V2 B-C strand-connecting loop. IMPORTANCE The levels of antibodies to the third variable region (V3) of the HIV envelope protein correlate with reduced HIV infection rates. Previous studies showed that V3 is often occluded, as it sits in a pocket of the envelope trimer on the surface of virions; however, the trimer is flexible, allowing occluded portions of the envelope (like V3) to flicker into an exposed position that binds antibodies. Here we provide a systematic interrogation of mechanisms by which single amino acid changes in various

  3. Structure-Function Studies with the Unique Hexameric Form II Ribulose-1,5-bisphosphate Carboxylase/Oxygenase (Rubisco) from Rhodopseudomonas palustris*

    PubMed Central

    Satagopan, Sriram; Chan, Sum; Perry, L. Jeanne; Tabita, F. Robert

    2014-01-01

    The first x-ray crystal structure has been solved for an activated transition-state analog-bound form II ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco). This enzyme, from Rhodopseudomonas palustris, assembles as a unique hexamer with three pairs of catalytic large subunit homodimers around a central 3-fold symmetry axis. This oligomer arrangement is unique among all known Rubisco structures, including the form II homolog from Rhodospirillum rubrum. The presence of a transition-state analog in the active site locked the activated enzyme in a “closed” conformation and revealed the positions of critical active site residues during catalysis. Functional roles of two form II-specific residues (Ile165 and Met331) near the active site were examined via site-directed mutagenesis. Substitutions at these residues affect function but not the ability of the enzyme to assemble. Random mutagenesis and suppressor selection in a Rubisco deletion strain of Rhodobacter capsulatus identified a residue in the amino terminus of one subunit (Ala47) that compensated for a negative change near the active site of a neighboring subunit. In addition, substitution of the native carboxyl-terminal sequence with the last few dissimilar residues from the related R. rubrum homolog increased the enzyme's kcat for carboxylation. However, replacement of a longer carboxyl-terminal sequence with termini from either a form III or a form I enzyme, which varied both in length and sequence, resulted in complete loss of function. From these studies, it is evident that a number of subtle interactions near the active site and the carboxyl terminus account for functional differences between the different forms of Rubiscos found in nature. PMID:24942737

  4. Structure-function relationships of the yeast fatty acid synthase: negative-stain, cryo-electron microscopy, and image analysis studies of the end views of the structure.

    PubMed

    Stoops, J K; Kolodziej, S J; Schroeter, J P; Bretaudiere, J P; Wakil, S J

    1992-07-15

    The yeast fatty acid synthase (M(r) = 2.5 x 10(6)) is organized in an alpha 6 beta 6 complex. In these studies, the synthase structure has been examined by negative-stain and cryo-electron microscopy. Side and end views of the structure indicate that the molecule, shaped similar to a prolate ellipsoid, has a high-density band of protein bisecting its major axis. Stained and frozen-hydrated average images of the end views show an excellent concordance and a hexagonal ring having three each alternating egg- and kidney-shaped features with low-protein-density protrusions extending outward from the egg-shaped features. Images also show that the barrel-like structure is not hollow but has a Y-shaped central core, which appears to make contact with the three egg-shaped features. Numerous side views of the structure give good evidence that the beta subunits have an archlike shape. We propose a model for the synthase that has point-group symmetry 32 and six equivalent sites of fatty acid synthesis. The protomeric unit is alpha 2 beta 2. The ends of each of the two archlike beta subunits interact with opposite sides of the two dichotomously arranged disclike alpha subunits. Three such protomeric units form the ring. We propose that the six fatty acid synthesizing centers are composed of two complementary half-alpha subunits and a beta subunit, an arrangement having all the partial activities of the multifunctional enzyme required for fatty acid synthesis. PMID:1631160

  5. In vivo structure-function studies of human hepatic lipase: the catalytic function rescues the lean phenotype of HL-deficient (hl−/−) mice

    PubMed Central

    Chen, Jeffrey; Kaiyala, Karl J; Lam, Jennifer; Agrawal, Nalini; Nguyen, Lisa; Ogimoto, Kayoko; Spencer, Dean; Morton, Gregory J; Schwartz, Michael W; Dichek, Helén L

    2015-01-01

    The lean body weight phenotype of hepatic lipase (HL)–deficient mice (hl−/−) suggests that HL is required for normal weight gain, but the underlying mechanisms are unknown. HL plays a unique role in lipoprotein metabolism performing bridging as well as catalytic functions, either of which could participate in energy homeostasis. To determine if both the catalytic and bridging functions or the catalytic function alone are required for the effect of HL on body weight, we studied (hl−/−) mice that transgenically express physiologic levels of human (h)HL (with catalytic and bridging functions) or a catalytically-inactive (ci)HL variant (with bridging function only) in which the catalytic Serine 145 was mutated to Alanine. As expected, HL activity in postheparin plasma was restored to physiologic levels only in hHL-transgenic mice (hl−/−hHL). During high-fat diet feeding, hHL-transgenic mice exhibited increased body weight gain and body adiposity relative to hl−/−ciHL mice. A similar, albeit less robust effect was observed in female hHL-transgenic relative to hl−/−ciHL mice. To delineate the basis for this effect, we determined cumulative food intake and measured energy expenditure using calorimetry. Interestingly, in both genders, food intake was 5–10% higher in hl−/−hHL mice relative to hl−/−ciHL controls. Similarly, energy expenditure was ∼10% lower in HL-transgenic mice after adjusting for differences in total body weight. Our results demonstrate that (1) the catalytic function of HL is required to rescue the lean body weight phenotype of hl−/− mice; (2) this effect involves complementary changes in both sides of the energy balance equation; and (3) the bridging function alone is insufficient to rescue the lean phenotype of hl−/−ciHL mice. PMID:25862097

  6. Proteomic approaches to study structure, functions and toxicity of legume seeds lectins. Perspectives for the assessment of food quality and safety.

    PubMed

    Nasi, Antonella; Picariello, Gianluca; Ferranti, Pasquale

    2009-04-13

    Lectins are a structurally diverse class of (glyco)proteins which bind mono- and oligosaccharides with high specificity and in a reversible way. For many years, the unique sugar binding properties of plant lectins have been exploited for the development of biochemical tools for glycoprotein isolation and characterisation, and the use of lectins as a glycoprofiling tool has became much more sophisticated with the advent of lectin microarrays, in which a panel of lectins are immobilized on a single chip for glycomic analysis. Among the numerous lectins studied so far, those from legumes represent the largest family. They can be present at relatively high amounts depending on genetic as well as environmental factors, and are accumulated especially in the seeds. For this reason, some lectins as the phytohemagglutinin from the common bean Phaseolus vulgaris constitute a possible risk, since consumption of raw or incorrectly processed beans has been shown to cause outbreaks of gastroenteritis, nausea and diarrhoea. On the other hand, for these anti-nutritional properties, bean extracts enriched in lectins or in lectin-related amylase inhibitors are also finding a growing use as active ingredients of "weight-blockers" in dietetic preparations for obesity treatment. Current methods to determine the lectin levels in foods are based on immunoenzymatic or toxicity tests, which are largely aspecific. Very recently, the availability of proteomic methodologies has allowed to start development and validation of sensitive and specific assays for detecting trace amounts of harmful lectins in either raw or processed foods. In this review, the main aspects of current and perspective applications of mass spectrometry and proteomic technologies to the structural characterisation of legumes are presented, with focus on issues related to detection, identification, and quantification of phytohemagglutinins relevant for their biochemical, immunological and toxicological aspects. PMID

  7. Structural-functional characterization of the cathodic haemoglobin of the conger eel Conger conger: molecular modelling study of an additional phosphate-binding site.

    PubMed Central

    Pellegrini, Mariagiuseppina; Giardina, Bruno; Verde, Cinzia; Carratore, Vito; Olianas, Alessandra; Sollai, Luigi; Sanna, Maria T; Castagnola, Massimo; di Prisco, Guido

    2003-01-01

    The protein sequence data for the alpha- and beta-chains have been deposited in the SWISS-PROT and TrEMBL protein knowledgebase under the accession numbers P83479 and P83478 respectively. The Conger conger (conger eel) haemoglobin (Hb) system is made of three components, one of which, the so-called cathodic Hb, representing approx. 20% of the total pigment, has been purified and characterized from both a structural and functional point of view. Stripped Hb showed a reverse Bohr effect, high oxygen affinity and slightly low cooperativity in the absence of any effector. Addition of saturating GTP strongly influences the pH dependence of the oxygen affinity, since the reverse Bohr effect, observed under stripped conditions, is converted into a small normal Bohr effect. A further investigation of the GTP effect on oxygen affinity, carried out by fitting its titration curve, demonstrated the presence of two independent binding sites. Therefore, on the basis of the amino acid sequence of the alpha- and beta-chains, which have been determined, a computer modelling study has been performed. The data suggest that C. conger cathodic Hb may bind organic phosphates at two distinct binding sites located along the central cavity of the tetramer by hydrogen bonds and/or electrostatic interactions with amino acid residues of both chains, which have been identified. Among these residues, the two Lys-alpha(G6) (where the letter refers to the haemoglobin helix and the number to the amino acid position in the helix) appear to have a key role in the GTP movement from the external binding region to the internal central cavity of the tetrameric molecule. PMID:12646043

  8. Structure/function studies of human immunodeficiency virus type 1 reverse transcriptase. Alanine scanning mutagenesis of an alpha-helix in the thumb subdomain.

    PubMed

    Beard, W A; Stahl, S J; Kim, H R; Bebenek, K; Kumar, A; Strub, M P; Becerra, S P; Kunkel, T A; Wilson, S H

    1994-11-11

    Human immunodeficiency virus type 1 reverse transcriptase has subunits of 66 and 51 kDa (p66 and p51, respectively). Structural studies indicate that each subunit consists of common subdomains. The polymerase domain of p66 forms a nucleic acid binding cleft, and, by analogy with a right hand, the subdomains are referred to as fingers, palm, and thumb (Kohlstaedt, L. A., Wang, J., Friedman, J. M., Rice, P. A., and Steitz, T. A. (1992) Science 256, 1783-1790). Residues 257-266 correspond to a highly conserved region of primary structure among retroviral pol genes. Crystallographic evidence indicates that these residues are in the thumb subdomain and form part of an alpha-helix (alpha H), which interacts with DNA (Jacobo-Molina, A., Ding, J., Nanni, R. G., Clark, A. D., Jr., Lu, X., Tantillo, C., Williams, R. L., Kamer, G., Ferris, A. L., Clark, P., Hizi, A., Hughes, S. H., and Arnold, E. (1993) Proc. Natl. Acad. Sci. U. S. A. 90, 6320-6324). To define the role of this region during catalytic cycling, we performed systematic site-directed mutagenesis from position 253 through position 271 by changing each residue, one by one, to alanine. Each mutant protein was expressed and purified, and their substrate-specific activities were surveyed. The results are consistent with alpha H (residues 255-268) of p66 interacting with the template and/or primer strand. The core of alpha H appears to play an important role in template-primer binding (residues Gln-258, Gly-262, and Trp-266), and in protein-protein interactions (residues Val-261 and Leu-264). The periodicity of the effects observed suggest that a segment of one face of alpha H interacts with the template-primer. The lower fidelity observed with alanine mutants of Gly-262 and Trp-266 correlated with an over 200-fold increase in the dissociation rate constant for template-primer relative to wild type enzyme and suggests that enzyme-DNA interactions in the template-primer stem are important fidelity determinants. PMID

  9. Proton structure functions at small x

    SciTech Connect

    Hentschinski, Martin

    2015-01-01

    Proton structure functions are measured in electron-proton collision through inelastic scattering of virtual photons with virtuality Q on protons; x denotes the momentum fraction carried by the struck parton. Proton structure functions are currently described with excellent accuracy in terms of scale dependent parton distribution functions, defined in terms of collinear factorization and DGLAP evolution in Q. With decreasing x however, parton densities increase and are ultimately expected to saturate. In this regime DGLAP evolution will finally break down and non-linear evolution equations w.r.t x are expected to take over. In the first part of the talk we present recent result on an implementation of physical DGLAP evolution. Unlike the conventional description in terms of parton distribution functions, the former describes directly the Q dependence of the measured structure functions. It is therefore physical insensitive to factorization scheme and scale ambiguities. It therefore provides a more stringent test of DGLAP evolution and eases the manifestation of (non-linear) small x effects. It however requires a precise measurement of both structure functions F2 and FL, which will be only possible at future facilities, such as an Electron Ion Collider. In the second part we present a recent analysis of the small x region of the combined HERA data on the structure function F2. We demonstrate that (linear) next-to-leading order BFKL evolution describes the effective Pomeron intercept, determined from the combined HERA data, once a resummation of collinear enhanced terms is included and the renormalization scale is fixed using the BLM optimal scale setting procedure. We also provide a detailed description of the Q and x dependence of the full structure functions F2 in the small x region, as measured at HERA. As a result, predictions for the structure function FL are found to be in agreement with the existing HERA

  10. Proton structure functions at small x

    DOE PAGESBeta

    Hentschinski, Martin

    2015-01-01

    Proton structure functions are measured in electron-proton collision through inelastic scattering of virtual photons with virtuality Q on protons; x denotes the momentum fraction carried by the struck parton. Proton structure functions are currently described with excellent accuracy in terms of scale dependent parton distribution functions, defined in terms of collinear factorization and DGLAP evolution in Q. With decreasing x however, parton densities increase and are ultimately expected to saturate. In this regime DGLAP evolution will finally break down and non-linear evolution equations w.r.t x are expected to take over. In the first part of the talk we present recentmore » result on an implementation of physical DGLAP evolution. Unlike the conventional description in terms of parton distribution functions, the former describes directly the Q dependence of the measured structure functions. It is therefore physical insensitive to factorization scheme and scale ambiguities. It therefore provides a more stringent test of DGLAP evolution and eases the manifestation of (non-linear) small x effects. It however requires a precise measurement of both structure functions F2 and FL, which will be only possible at future facilities, such as an Electron Ion Collider. In the second part we present a recent analysis of the small x region of the combined HERA data on the structure function F2. We demonstrate that (linear) next-to-leading order BFKL evolution describes the effective Pomeron intercept, determined from the combined HERA data, once a resummation of collinear enhanced terms is included and the renormalization scale is fixed using the BLM optimal scale setting procedure. We also provide a detailed description of the Q and x dependence of the full structure functions F2 in the small x region, as measured at HERA. As a result, predictions for the structure function FL are found to be in agreement with the existing HERA data.« less

  11. Autotaxin: structure-function and signaling

    PubMed Central

    Perrakis, Anastassis; Moolenaar, Wouter H.

    2014-01-01

    Autotaxin (ATX), or ecto-nucleotide pyrophosphatase/phosphodiesterase-2, is a secreted lysophospholipase D (lysoPLD) that hydrolyzes extracellular lysophospholipids into the lipid mediator lysophosphatidic acid (LPA), a ligand for specific G protein-coupled receptors. ATX-LPA signaling is essential for development and has been implicated in a great diversity of (patho)physiological processes, ranging from lymphocyte homing to tumor progression. Structural and functional studies have revealed what makes ATX a unique lysoPLD, and how secreted ATX binds to its target cells. The ATX catalytic domain shows a characteristic bimetallic active site followed by a shallow binding groove that can accommodate nucleotides as well as the glycerol moiety of lysophospholipids, and by a deep lipid-binding pocket. In addition, the catalytic domain has an open tunnel of unknown function adjacent to the active site. Here, we discuss our current understanding of ATX structure-function relationships and signaling mechanisms, and how ATX isoforms use distinct mechanisms to target LPA production to the plasma membrane, notably binding to integrins and heparan sulfate proteoglycans. We also briefly discuss the development of drug-like inhibitors of ATX. PMID:24548887

  12. Degradation of Bimetallic Model Electrocatalysts ___ an in situ XAS Study

    SciTech Connect

    Friebel, Daniel

    2011-06-22

    One of the major challenges in the development of clean energy fuel cells is the performance degradation of the electrocatalyst, which, apart from poisoning effects, can suffer from corrosion due to its exposure to a harsh environment under high potentials. In this communication, we demonstrate how interactions of Pt with a transition metal support affect not only, as commonly intended, the catalytic activity, but also the reactivity of Pt towards oxide formation or dissolution. We use two well-defined single-crystal model systems, Pt/Rh(111) and Pt/Au(111) and a unique x-ray spectroscopy technique with enhanced energy resolution to monitor the potential-dependent oxidation state of Pt, and find two markedly different oxidation mechanisms on the two different substrates. This information can be of great significance for future design of more active and more stable catalysts. We have studied the potential-induced degradation of Pt monolayer model electrocatalysts on Rh(111) and Au(111) single-crystal substrates. The anodic formation of Pt oxides was monitored using in situ high energy resolution fluorescence detection x-ray absorption spectroscopy (HERFD XAS). Although Pt was deposited on both substrates in a three-dimensional island growth mode, we observed remarkable differences during oxide formation that can only be understood in terms of strong Pt-substrate interactions throughout the Pt islands. Anodic polarization of Pt/Rh(111) up to +1.6 V vs. RHE (reversible hydrogen electrode) leads to formation an incompletely oxidized passive layer, whereas formation of PtO2 and partial Pt dissolution is observed for Pt/Au(111).

  13. Remedition case studies: Thermal desorption, soil washing, and in situ vitrification

    SciTech Connect

    1995-03-01

    The purpose of this report is to provide case studies of site cleanup projects utilizing thermal desorption, soil washing, and in situ vitrification. This volume contains reports on projects using thermal desorption, including six completed applications at sites contaminated with PCBs, pesticides, or chlorinated aliphatics. Two projects in this volume used soil washing and in situ vitrification technologies.

  14. Oxidative Dehydrogenation on Nanocarbon: Intrinsic Catalytic Activity and Structure-Function Relationships.

    PubMed

    Qi, Wei; Liu, Wei; Guo, Xiaoling; Schlögl, Robert; Su, Dangsheng

    2015-11-01

    Physical and chemical insights into the nature and quantity of the active sites and the intrinsic catalytic activity of nanocarbon materials in alkane oxidative dehydrogenation (ODH) reactions are reported using a novel in situ chemical titration process. A study on the structure-function relationship reveals that the active sites are identical both in nature and function on various nanocarbon catalysts. Additionally, the quantity of the active sites could be used as a metric to normalize the reaction rates, and thus to evaluate the intrinsic activity of nanocarbon catalysts. The morphology of the nanocarbon catalysts at the microscopic scale exhibits a minor influence on their intrinsic ODH catalytic activity. The number of active sites calculated from the titration process indicates the number of catalytic centers that are active (that is, working) under the reaction conditions. PMID:26388451

  15. In-situ spectroscopic studies of electrochromic tungsten oxide films

    NASA Astrophysics Data System (ADS)

    Ozer, Nilgun; Demirbas, Muharrem; Ozyurt, Secuk

    2001-11-01

    Tungsten oxide thin films were prepared using an ethanolic solution of tungsten hexachloride (WCl6) by sol-gel spin coating. The films were spin coated on indium tin oxide (ITO) coated glass substrate at temperatures in the range of 100 to 450 degree(s)C. The films were characterized by x-ray diffractometry (XRD), scanning electron microscopy (SEM) UV- visible spectroscopy and cyclic voltammetry (CV). XRD showed that they had a polycrystalline WO3 structure for heat treatment temperatures at above 350 degree(s)C. The SEM examinations showed that the surface texture was very uniform and homogeneous. In situ electrochemical reduction of WO3/ITO (2M HCl) produced a blue color in less than a second. Coloration efficiency (CE) was found to be 21 cm2/mC. In situ spectroscopic investigations showed that these films could be used as a working electrode in electrochromic devices.

  16. Structural Functionalism as a Heuristic Device.

    ERIC Educational Resources Information Center

    Chilcott, John H.

    1998-01-01

    Argues that structural functionalism as a method for conducting fieldwork and as a format for the analysis of ethnographic data remains a powerful model, one that is easily understood by professional educators. As a heuristic device, functionalist theory can help in the solution of a problem that is otherwise incapable of theoretical…

  17. Feminine Faces of Leadership: Beyond Structural- Functionalism?

    ERIC Educational Resources Information Center

    Fennell, Hope-Arlene

    1999-01-01

    Reviews four philosophical leadership perspectives: structural-functionalism, constructivism, critical theory, and feminism. Explores the leadership phenomenon through the eyes of six women principals. Although the behaviors of all six fall within a structural-functionalist perspective, each is attempting to construct inclusive, positive, and…

  18. 2004 Structural, Function and Evolutionary Genomics

    SciTech Connect

    Douglas L. Brutlag Nancy Ryan Gray

    2005-03-23

    This Gordon conference will cover the areas of structural, functional and evolutionary genomics. It will take a systematic approach to genomics, examining the evolution of proteins, protein functional sites, protein-protein interactions, regulatory networks, and metabolic networks. Emphasis will be placed on what we can learn from comparative genomics and entire genomes and proteomes.

  19. Structure functions: Their status and implications

    SciTech Connect

    Hinchliffe, I.

    1988-09-29

    I discuss the current status of structure functions. Attention is given to the uncertainties in them and the implications of these uncertainties for experimental predictions. I indicate which experiments are capable of removing these uncertainties. 17 refs., 17 figs., 1 tab.

  20. Towards microfluidic reactors for in situ synchrotron infrared studies

    NASA Astrophysics Data System (ADS)

    Silverwood, I. P.; Al-Rifai, N.; Cao, E.; Nelson, D. J.; Chutia, A.; Wells, P. P.; Nolan, S. P.; Frogley, M. D.; Cinque, G.; Gavriilidis, A.; Catlow, C. R. A.

    2016-02-01

    Anodically bonded etched silicon microfluidic devices that allow infrared spectroscopic measurement of solutions are reported. These extend spatially well-resolved in situ infrared measurement to higher temperatures and pressures than previously reported, making them useful for effectively time-resolved measurement of realistic catalytic processes. A data processing technique necessary for the mitigation of interference fringes caused by multiple reflections of the probe beam is also described.

  1. Holographic microscopy for in situ studies of microorganism motility

    NASA Astrophysics Data System (ADS)

    Nadeau, J.; Hu, S.; Jericho, S.; Lindensmith, C.

    2011-12-01

    Robust technologies for the detection and identification of microorganisms at low concentrations in complex liquid media are needed for numerous applications: environmental and medical microbiology, food safety, and for the search for microbial life elsewhere in the Solar System. The best current method for microbial enumeration is specific labeling with fluorescent dyes followed by high-resolution light microscopy. However, fluorescent techniques are difficult to use in situ in extreme environments (such as the Arctic and Antarctic or the open ocean) due to the fragility of the instruments and their high power demands. In addition, light microscopic techniques rarely provide insight into microbial motility behaviors. Tracking single cells would provide important insight into the physics of micron-scale motility as well as into key microbial phenomena such as surface attachment and invasiveness. An alternative to traditional light microscopy that is attracting increasing attention is holographic microscopy. Holographic microscopy works by illuminating the object of interest with coherent light from a laser. The light reflected from (or transmitted through) the object is then combined with a coherent reference beam to create an interference pattern that contains the phase and intensity information required to reconstruct a three dimensional image of the object. The interference pattern is recorded on a high resolution detector and can be used to computationally reconstruct a 3D image of the object. The lateral resolution of the image depends upon the wavelength of the light used, the laser power, camera quality, and external noise sources (vibration, stray light, and so forth). Although the principle is simple, technological barriers have prevented wider use of holographic microscopy. Laser sources and CCD cameras with the appropriate properties have only very recently become affordable. In addition, holographic microscopy leads to large data sets that are

  2. Evolving Technologies for In-Situ Studies of Mars Ice

    NASA Technical Reports Server (NTRS)

    Carsey, F. D.; Hecht, M. H.

    2003-01-01

    Icy sites on Mars continue to be of high scientific importance. These sites include the polar caps, the southern mid-latitude subsurface permafrost, and the seasonal frost. These sites have interest due to their roles in climate processes, past climates, surface and near-surface water, astrobiology, geomorphology, and other topics. As is the case for many planetary features, remote sensing, while of great value, cannot answer all questions; in-situ examination is essential, and the motivation for in-situ observations generally leads to the subsurface, which, fortunately, is accessible on Mars. It is clear in fact that a Mars polar cap subsurface mission is both scientifically compelling and practical. Recent data from orbiting platforms has provided a remarkable level of information about the Mars ice caps; we know, for example, the size, shape and annual cycle of the cap topography as well as we know that of Earth, and we have more information on stratification that we have of, for example, the ice of East Antarctica. To understand the roles that the Mars polar caps play, it is necessary to gather information on the ice cap surface, strata, composition and bed. In this talk the status of in-situ operations and observations will be summarized, and, since we have conveniently at hand another planet with polar caps, permafrost and ice, the role of testing and validation of experimental procedures on Earth will be addressed.

  3. Semiconductor nanorod self-assembly at the liquid/air interface studied by in situ GISAXS and ex situ TEM.

    PubMed

    Pietra, Francesca; Rabouw, Freddy T; Evers, Wiel H; Byelov, Dima V; Petukhov, Andrei V; de Mello Donegá, Celso; Vanmaekelbergh, Daniël

    2012-11-14

    We study the self-assembly of colloidal CdSe/CdS nanorods (NRs) at the liquid/air interface combining time-resolved in situ grazing-incidence small angle X-ray scattering (GISAXS) and ex situ transmission electron microscopy (TEM). Our study shows that NR superstructure formation occurs at the liquid/air interface. Short NRs self-assemble into micrometers long tracks of NRs lying side by side flat on the surface. In contrast, longer NRs align vertically into ordered superstructures. Systematic variation of the NR length and initial concentration of the NR dispersion allowed us to tune the orientation of the NRs in the final superstructure. With GISAXS, we were able to follow the dynamics of the self-assembly. We propose a model of hierarchical self-organization that provides a basis for the understanding of the length-dependent self-organization of NRs at the liquid/air interface. This opens the way to new materials based on NR membranes and anisotropic thin films. PMID:23038984

  4. Remediation case studies: In situ soil treatment technologies (soil vapor extraction, thermal processes). Volume 8

    SciTech Connect

    1998-09-01

    The case studies present available cost and performance information for full-scale remediation efforts. The studies contain varying levels of detail, reflecting the differences in the availability of data and information. The case studies in this volume describe 14 applications of soil vapor extraction (SVE) and in situ thermal processes. These include 10 full-scale and one pilot-scale SVE applications used to treat soil contaminated with chlorinated solvents and petroleum hydrocarbons. Three of these applications involved treatment or containment of both contaminated soil and groundwater through a combination of SVE, air sparging, groundwater extraction, and/or in situ bioremediation technologies. One case study describes a photolytic technology demonstrated for treatment of contaminated vapors from an SVE system. In addition, this volume describes two in situ thermal treatment applications, one used to recover free and residual coal tar, and one that was a demonstration of an in situ process to desorb PCBs from soil.

  5. Geometrical scaling in charm structure function ratios

    NASA Astrophysics Data System (ADS)

    Boroun, G. R.; Rezaei, B.

    2014-09-01

    By using a Laplace-transform technique, we solve the next-to-leading-order master equation for charm production and derive a compact formula for the ratio Rc = FLccbar/F2ccbar, which is useful for extracting the charm structure function from the reduced charm cross section, in particular, at DESY HERA, at small x. Our results show that this ratio is independent of x at small x. In this method of determining the ratios, we apply geometrical scaling in charm production in deep inelastic scattering (DIS). Our analysis shows that the renormalization scales have a sizable impact on the ratio Rc at high Q2. Our results for the ratio of the charm structure functions are in a good agreement with some phenomenological models.

  6. Nuclear diffractive structure functions at high energies

    SciTech Connect

    Marquet,C.; Kowalski, H.; Lappi, T.; Venugopalan, R.

    2008-08-08

    A future high-energy electron-ion collider would explore the non-linear weakly-coupled regime of QCD, and test the Color Glass Condensate (CGC) approach to high-energy scattering. Hard diffraction in deep inelastic scattering off nuclei will provide many fundamental measurements. In this work, the nuclear diffractive structure function F{sub 2,A}{sup D} is predicted in the CGC framework, and the features of nuclear enhancement and suppression are discussed.

  7. Structure function calculations for Ostwald Ripening processes

    NASA Technical Reports Server (NTRS)

    Hassan, Razi A.

    1990-01-01

    A program for computing the structure function for configurations involved in Ostwald Ripening was written. The basic algorithms are derived from a mathematical analysis of a two-dimensional model system developed by Bortz, et. al. (1974). While it is expected that the values form the computer simulations will reflect Ostwald Ripening, at this point the program is still being tested. Some preliminary runs seem to justify the expectations.

  8. Purification of integral outer-membrane protein OmpC, a surface antigen from Salmonella typhi for structure-function studies: a method applicable to enterobacterial major outer-membrane protein.

    PubMed

    Arockiasamy, A; Krishnaswamy, S

    2000-07-15

    Extraction of the outer-membrane porin, OmpC, from Salmonella typhi Ty21a was done by using a modified salt-extraction procedure. It was possible to extract only the major outer-membrane protein (OMP) from the crude membrane using this method. Aberrant lipopolysaccharide (LPS) production in the galE mutant Ty21a has resulted in more isoforms of OmpC and subsequently led to anomalous mobility in SDS-PAGE. The purity of the preparation was confirmed by denaturing urea SDS-PAGE and N-terminal sequencing. The major OMP extracts had LPS of both bound and free forms. The free form of LPS could be removed by gel filtration and the bound form, largely, was removed using ion-exchange chromatography and by passing through ultrafiltration devices. This method has been used to extract the native trimer of OmpC, the major OMP, in a large scale, for structure-function studies. S. typhi Ty21a OmpC preparation yielded reproducible diffraction-quality crystals. Extracts of porin from wild-type Escherichia coli HB101, grown under high osmolarity conditions, showed a single species of OMP on SDS-PAGE. This suggests the possible application of the method to other gram-negative bacterial porins. PMID:10929809

  9. Spin Structure Functions from Electron Scattering

    SciTech Connect

    Seonho Choi

    2012-09-01

    The spin structure of the nucleon can play a key testing ground for Quantum Chromo-Dynamics (QCD) at wide kinematic ranges from smaller to large four momentum transfer Q{sup 2}. The pioneering experiments have confirmed several QCD sum rules at high Q{sup 2} where a perturbative picture holds. For a full understanding of QCD at various scales, various measurements were made at intermediate and small Q{sup 2} region and their interpretation would be a challenging task due to the non-perturbative nature. Jefferson Lab has been one of the major experimental facilities for the spin structure with its polarized electron beams and various polarized targets. A few QCD sum rules have been compared with the measured spin structure functions g{sub 1}(x, Q{sup 2}) and g{sub 2}(x, Q{sup 2}) at low Q{sup 2} and surprising results have been obtained for the spin polarizabilities, {gamma}{sub 0} and {delta}{sub LT} . As for the proton spin structure functions, the lack of data for g{sub 2}(x,Q{sup 2}) structure functions has been complemented with a new experiment at Jefferson Lab, SANE. The results from SANE will provide a better picture of the proton spin structure at a wide kinematic range in x and Q{sup 2}.

  10. MOLAB, a Mobile Laboratory for In Situ Non-Invasive Studies in Arts and Archaeology

    NASA Astrophysics Data System (ADS)

    Brunetti, B. G.; Matteini, Mauro; Miliani, C.; Pezzati, L.; Pinna, D.

    Mobile laboratory (MOLAB) is a unique joint collection of portable equipment for non-destructive in situ measurements. MOLAB activities are carried out within the frame of the Eu-ARTECH Integrated Infrastructure Initiative of the sixth F.P. In situ measurement is quite useful because it eliminates any risk connected to moving artworks or other precious objects to a laboratory. MOLAB instruments are accessible to European researchers through a peer-review selection of proposals. Starting from July 2004, MOLAB enabled non-destructive in situ studies of many precious artworks, such as paintings by Perugino, Raphael and Leonardo.

  11. In situ anodization of aluminum surfaces studied by x-ray reflectivity and electrochemical impedance spectroscopy

    SciTech Connect

    Bertram, F. Evertsson, J.; Messing, M. E.; Mikkelsen, A.; Lundgren, E.; Zhang, F.; Pan, J.; Carlà, F.; Nilsson, J.-O.

    2014-07-21

    We present results from the anodization of an aluminum single crystal [Al(111)] and an aluminum alloy [Al 6060] studied by in situ x-ray reflectivity, in situ electrochemical impedance spectroscopy and ex situ scanning electron microscopy. For both samples, a linear increase of oxide film thickness with increasing anodization voltage was found. However, the slope is much higher in the single crystal case, and the break-up of the oxide film grown on the alloy occurs at a lower anodization potential than on the single crystal. The reasons for these observations are discussed as are the measured differences observed for x-ray reflectivity and electrochemical impedance spectroscopy.

  12. In situ anodization of aluminum surfaces studied by x-ray reflectivity and electrochemical impedance spectroscopy

    NASA Astrophysics Data System (ADS)

    Bertram, F.; Zhang, F.; Evertsson, J.; Carlà, F.; Pan, J.; Messing, M. E.; Mikkelsen, A.; Nilsson, J.-O.; Lundgren, E.

    2014-07-01

    We present results from the anodization of an aluminum single crystal [Al(111)] and an aluminum alloy [Al 6060] studied by in situ x-ray reflectivity, in situ electrochemical impedance spectroscopy and ex situ scanning electron microscopy. For both samples, a linear increase of oxide film thickness with increasing anodization voltage was found. However, the slope is much higher in the single crystal case, and the break-up of the oxide film grown on the alloy occurs at a lower anodization potential than on the single crystal. The reasons for these observations are discussed as are the measured differences observed for x-ray reflectivity and electrochemical impedance spectroscopy.

  13. Polarized Structure Functions: Proton/Deuteron Measurements in Hall C

    SciTech Connect

    Oscar A. Rondon

    2005-02-01

    The study of the nucleon polarized structure functions has matured beyond the inclusive measurements of the past to the investigation of all eight quark distribution functions in the nucleon. Jefferson Lab's Hall C program of polarized structure functions studies started with a measurement of the proton and deuteron spin structure in the resonances at Q2 {approx} 1.3 [GeV/c]2. This work will be extended for the proton to more than 5 [GeV/c]2 for both DIS and the resonances in the upcoming SANE experiment. SANE will use a novel non-magnetic very large solid angle detector, BETA. Semi-inclusive asymmetries will be measured to determine the flavor composition of the nucleon spin in the recently approved Semi-SANE experiment. The 11 GeV energy upgrade will open new opportunities to study other functions, such as the transversity, Collins and Sievers functions, using vertical polarized targets.

  14. Polarized Structure Functions: Proton/Deuteron Measurements in Hall C

    SciTech Connect

    Rondon, Oscar A.

    2005-02-10

    The study of the nucleon polarized structure functions has matured beyond the inclusive measurements of the past to the investigation of all eight quark distribution functions in the nucleon. Jefferson Lab's Hall C program of polarized structure functions studies started with a measurement of the proton and deuteron spin structure in the resonances at Q2 {approx} 1.3 [GeV/c]2. This work will be extended for the proton to more than 5 [GeV/c]2 for both DIS and the resonances in the upcoming SANE experiment. SANE will use a novel non-magnetic very large solid angle detector, BETA. Semi-inclusive asymmetries will be measured to determine the flavor composition of the nucleon spin in the recently approved Semi -- SANE experiment. The 11 GeV energy upgrade will open new opportunities to study other functions, such as the transversity, Collins and Sievers functions, using vertical polarized targets.

  15. In situ studies of microbial inactivation during high pressure processing

    NASA Astrophysics Data System (ADS)

    Maldonado, Jose Antonio; Schaffner, Donald W.; Cuitiño, Alberto M.; Karwe, Mukund V.

    2016-01-01

    High pressure processing (HPP) has been shown to reduce microbial concentration in foods. The mechanisms of microbial inactivation by HPP have been associated with damage to cell membranes. The real-time response of bacteria to HPP was measured to elucidate the mechanisms of inactivation, which can aid in designing more effective processes. Different pressure cycling conditions were used to expose Enterobacter aerogenes cells to HPP. Propidium iodide (PI) was used as a probe, which fluoresces after penetrating cells with damaged membranes and binding with nucleic acids. A HPP vessel with sapphire windows was used for measuring fluorescence in situ. Membrane damage was detected during pressurization and hold time, but not during depressurization. The drop in fluorescence was larger than expected after pressure cycles at higher pressure and longer times. This indicated possible reversible disassociation of ribosomes resulting in additional binding of PI to exposed RNA under pressure and its release after depressurization.

  16. Setup for in situ x-ray diffraction study of swift heavy ion irradiated materials

    SciTech Connect

    Kulriya, P. K.; Singh, F.; Tripathi, A.; Ahuja, R.; Kothari, A.; Dutt, R. N.; Mishra, Y. K.; Kumar, Amit; Avasthi, D. K.

    2007-11-15

    An in situ x-ray diffraction (XRD) setup is designed and installed in the materials science beam line of the Pelletron accelerator at the Inter-University Accelerator Centre for in situ studies of phase change in swift heavy ion irradiated materials. A high vacuum chamber with suitable windows for incident and diffracted X-rays is integrated with the goniometer and the beamline. Indigenously made liquid nitrogen (LN{sub 2}) temperature sample cooling unit is installed. The snapshots of growth of particles with fluence of 90 MeV Ni ions were recorded using in situ XRD experiment, illustrating the potential of this in situ facility. A thin film of C{sub 60} was used to test the sample cooling unit. It shows that the phase of the C{sub 60} film transforms from a cubic lattice (at room temperature) to a fcc lattice at around T=255 K.

  17. A no extensive statistical model for the nucleon structure function

    SciTech Connect

    Trevisan, Luis A.; Mirez, Carlos

    2013-03-25

    We studied an application of nonextensive thermodynamics to describe the structure function of nucleon, in a model where the usual Fermi-Dirac and Bose-Einstein energy distribution were replaced by the equivalent functions of the q-statistical. The parameters of the model are given by an effective temperature T, the q parameter (from Tsallis statistics), and two chemical potentials given by the corresponding up (u) and down (d) quark normalization in the nucleon.

  18. a Nonextensive Statistical Model for the Nucleon Structure Function

    NASA Astrophysics Data System (ADS)

    Trevisan, Luis Augusto; Mirez, Carlos

    2013-07-01

    We studied an application of nonextensive thermodynamics to describe the structure function of nucleon, in a model where the usual Fermi-Dirac and Bose-Einstein energy distribution were replaced by the equivalent functions of the q-statistical. The parameters of the model are given by an effective temperature T, the q parameter (from Tsallis statistics), and two chemical potentials given by the corresponding up (u) and down (d) quark normalizations in the nucleon.

  19. A no extensive statistical model for the nucleon structure function

    NASA Astrophysics Data System (ADS)

    Trevisan, Luis A.; Mirez, Carlos

    2013-03-01

    We studied an application of nonextensive thermodynamics to describe the structure function of nucleon, in a model where the usual Fermi-Dirac and Bose-Einstein energy distribution were replaced by the equivalent functions of the q-statistical. The parameters of the model are given by an effective temperature T, the q parameter (from Tsallis statistics), and two chemical potentials given by the corresponding up (u) and down (d) quark normalization in the nucleon.

  20. Nucleon structure functions from constituent quark

    NASA Astrophysics Data System (ADS)

    Khorramian, Ali N.; Arash, Firooz

    1999-10-01

    We have used a constituent quarks model to describe the nucleon structure function, F2( χ, Q2), for a wide range of χ=[10 -6,1] and Q2 = [0.5, 5000] GeV2. We have found that although F2 rises as χ decreases, but there exists some χ0 ≤ 10 -4 - 10 -5, below which the rise of F2 subsides drastically and hence, exhibits an almost flat behavior, compatible with the latest results from HERA, at least for low Q2.

  1. Alterations in juvenile flatfish gill epithelia induced by sediment-bound toxicants: A comparative in situ and ex situ study.

    PubMed

    Martins, Carla; Alves de Matos, António P; Costa, Maria H; Costa, Pedro M

    2015-12-01

    Juvenile Solea senegalensis were exposed in the laboratory (ex situ) and field (in situ) to different sediments of a moderately impacted estuary (the Sado, Portugal) for 28 days. A qualitative histopathological screening yielded scant lesions to gills, albeit alterations such as epithelial hyperplasia being evident and more frequent in fish exposed ex situ. Fully quantitative traits, namely chloride and goblet cell count and size revealed differences between the two bioassay approaches, with ex situ experiments likely enhancing bioavailability of toxicants. Chloride cells endured autolytic processes that could, at least in part, relate to contamination by mixed metals and polycyclic aromatic hydrocarbons (PAHs). Goblet cells did not reveal changes in the chemistry of mucous. Still, their number and size was reduced in fish exposed ex situ to the sediments most contaminated by PAHs, with evidence for adaptation. Also, copper histochemistry revealed the potential role of mucocytes in the regulation of metals. PMID:26518455

  2. A-dependence of weak nuclear structure functions

    SciTech Connect

    Haider, H.; Athar, M. Sajjad; Simo, I. Ruiz

    2015-05-15

    Effect of nuclear medium on the weak structure functions F{sub 2}{sup A}(x, Q{sup 2}) and F{sub 3}{sup A}(x, Q{sup 2}) have been studied using charged current (anti)neutrino deep inelastic scattering on various nuclear targets. Relativistic nuclear spectral function which incorporate Fermi motion, binding and nucleon correlations are used for the calculations. We also consider the pion and rho meson cloud contributions calculated from a microscopic model for meson-nucleus self-energies. Using these structure functions, F{sub i}{sup A}/F{sub i}{sup proton} and F{sub i}{sup A}/F{sub i}{sup deuteron}(i=2,3, A={sup 12}C, {sup 16}O, CH and H{sub 2}O) are obtained.

  3. Miniaturized Environmental Scanning Electron Microscope for In Situ Planetary Studies

    NASA Technical Reports Server (NTRS)

    Gaskin, Jessica; Abbott, Terry; Medley, Stephanie; Gregory, Don; Thaisen, Kevin; Taylor , Lawrence; Ramsey, Brian; Jerman, Gregory; Sampson, Allen; Harvey, Ralph

    2010-01-01

    The exploration of remote planetary surfaces calls for the advancement of low power, highly-miniaturized instrumentation. Instruments of this nature that are capable of multiple types of analyses will prove to be particularly useful as we prepare for human return to the moon, and as we continue to explore increasingly remote locations in our Solar System. To this end, our group has been developing a miniaturized Environmental-Scanning Electron Microscope (mESEM) capable of remote investigations of mineralogical samples through in-situ topographical and chemical analysis on a fine scale. The functioning of an SEM is well known: an electron beam is focused to nanometer-scale onto a given sample where resulting emissions such as backscattered and secondary electrons, X-rays, and visible light are registered. Raster scanning the primary electron beam across the sample then gives a fine-scale image of the surface topography (texture), crystalline structure and orientation, with accompanying elemental composition. The flexibility in the types of measurements the mESEM is capable of, makes it ideally suited for a variety of applications. The mESEM is appropriate for use on multiple planetary surfaces, and for a variety of mission goals (from science to non-destructive analysis to ISRU). We will identify potential applications and range of potential uses related to planetary exploration. Over the past few of years we have initiated fabrication and testing of a proof-of-concept assembly, consisting of a cold-field-emission electron gun and custom high-voltage power supply, electrostatic electron-beam focusing column, and scanning-imaging electronics plus backscatter detector. Current project status will be discussed. This effort is funded through the NASA Research Opportunities in Space and Earth Sciences - Planetary Instrument Definition and Development Program.

  4. Experimental study on neptunium migration under in situ geochemical conditions

    NASA Astrophysics Data System (ADS)

    Kumata, M.; Vandergraaf, T. T.

    1998-12-01

    Results are reported for migration experiments performed with Np under in situ geochemical conditions over a range of groundwater flow rates in columns of crushed rock in a specially designed facility at the 240-level of the Underground Research Laboratory (URL) near Pinawa, Manitoba, Canada. This laboratory is situated in an intrusive granitic rock formation, the Lac du Bonnet batholith. Highly altered granitic rock and groundwater were obtained from a major subhorizontal fracture zone at a depth of 250 m in the URL. The granite was wet-crushed and wet-sieved with groundwater from this fracture zone. The 180-850-μm size fraction was selected and packed in 20-cm long, 2.54-cm in diameter Teflon™-lined stainless steel columns. Approximately 30-ml vols of groundwater containing 3HHO and 237Np were injected into the columns at flow rates of 0.3, 1, and 3 ml/h, followed by elution with groundwater, obtained from the subhorizontal fracture, at the same flow rates, for a period of 95 days. Elution profiles for 3HHO were obtained, but no 237Np was detected in the eluted groundwater. After terminating the migration experiments, the columns were frozen, the column material was removed and cut into twenty 1-cm thick sections and each section was analyzed by gamma spectrometry. Profiles of 237Np were obtained for the three columns. A one-dimensional transport model was fitted to the 3HHO breakthrough curves to obtain flow parameters for this experiment. These flow parameters were in turn applied to the 237Np concentration profiles in the columns to produce sorption and dispersion coefficients for Np. The results show a strong dependence of retardation factors ( Rf) on flow rate. The decrease in the retarded velocity of the neptunium ( Vn) varied over one order of magnitude under the geochemical conditions for these experiments.

  5. Structure, Function and On-Off Switching of a Core Unit Contact between CheA Kinase and CheW Adaptor Protein in the Bacterial Chemosensory Array: A Disulfide Mapping and TAM-IDS Study

    PubMed Central

    Natale, Andrew M.; Duplantis, Jane L.; Piasta, Kene N.; Falke, Joseph J.

    2014-01-01

    The ultrasensitive, ultrastable bacterial chemosensory array of Escherichia coli and Salmonella typhimurium is representative of the large, conserved family of sensory arrays that control the cellular chemotaxis of motile bacteria and Archaea. The core framework of the membrane-bound array is a lattice assembled from three components: a transmembrane receptor, a cytoplasmic His kinase (CheA), and a cytoplasmic adaptor protein (CheW). Structural studies in the field have revealed the global architecture of the array and complexes between specific components, but much remains to be learned about the essential protein-protein interfaces that define array structure and transmit signals between components. This study has focused on the structure, function and on-off switching of a key contact between the kinase and adaptor proteins in the working, membrane-bound array. Specifically, the study addressed interface 1 in the putative kinase-adaptor ring where subdomain 1 of the kinase regulatory domain contacts subdomain 2 of the adaptor protein. Two independent approaches – disulfide mapping and site-directed Trp and Ala mutagenesis – were employed to (i) test the structural model of interface 1 and (ii) investigate its functional roles in both stable kinase incorporation and receptor-regulated kinase on-off switching. Studies were carried out in functional, membrane-bound arrays or in live cells. The findings reveal that crystal structures of binary and ternary complexes accurately depict the native interface in its kinase-activating on state. Furthermore, the findings indicate that at least part of the interface becomes less closely packed in its kinase-inhibiting off state. Together, the evidence shows the interface has a dual structural and signaling function that is crucial for stable kinase incorporation into the array, for kinase activation in the array on state, and likely for attractant-triggered kinase on-off switching. A model is presented that describes the

  6. Time Variability of Quasars: the Structure Function Variance

    NASA Astrophysics Data System (ADS)

    MacLeod, C.; Ivezić, Ž.; de Vries, W.; Sesar, B.; Becker, A.

    2008-12-01

    Significant progress in the description of quasar variability has been recently made by employing SDSS and POSS data. Common to most studies is a fundamental assumption that photometric observations at two epochs for a large number of quasars will reveal the same statistical properties as well-sampled light curves for individual objects. We critically test this assumption using light curves for a sample of ~2,600 spectroscopically confirmed quasars observed about 50 times on average over 8 years by the SDSS stripe 82 survey. We find that the dependence of the mean structure function computed for individual quasars on luminosity, rest-frame wavelength and time is qualitatively and quantitatively similar to the behavior of the structure function derived from two-epoch observations of a much larger sample. We also reproduce the result that the variability properties of radio and X-ray selected subsamples are different. However, the scatter of the variability structure function for fixed values of luminosity, rest-frame wavelength and time is similar to the scatter induced by the variance of these quantities in the analyzed sample. Hence, our results suggest that, although the statistical properties of quasar variability inferred using two-epoch data capture some underlying physics, there is significant additional information that can be extracted from well-sampled light curves for individual objects.

  7. Measurement of inclusive spin structure functions of the deuteron

    NASA Astrophysics Data System (ADS)

    Yun, J.; Kuhn, S. E.; Dodge, G. E.; Forest, T. A.; Taiuti, M.; Adams, G. S.; Amaryan, M. J.; Anciant, E.; Anghinolfi, M.; Asavapibhop, B.; Asryan, G.; Audit, G.; Auger, T.; Avakian, H.; Barrow, S.; Battaglieri, M.; Beard, K.; Bektasoglu, M.; Bertozzi, W.; Bianchi, N.; Biselli, A. S.; Boiarinov, S.; Bosted, P.; Bouchigny, S.; Bradford, R.; Branford, D.; Brooks, W. K.; Bueltmann, S.; Burkert, V. D.; Butuceanu, C.; Calarco, J. R.; Carman, D. S.; Carnahan, B.; Cetina, C.; Ciciani, L.; Cole, P. L.; Coleman, A.; Connelly, J.; Cords, D.; Corvisiero, P.; Crabb, D.; Crannell, H.; Cummings, J.; Sanctis, E. De; Vita, R. De; Degtyarenko, P. V.; Demirchyan, R. A.; Denizli, H.; Dennis, L. C.; Dharmawardane, K. V.; Djalali, C.; Domingo, J.; Doughty, D.; Dragovitsch, P.; Dugger, M.; Dytman, S.; Eckhause, M.; Efremenko, Y. V.; Egiyan, H.; Egiyan, K. S.; Elouadrhiri, L.; Empl, A.; Farhi, L.; Fatemi, R.; Feuerbach, R. J.; Ficenec, J.; Fissum, K.; Freyberger, A.; Frolov, V.; Funsten, H.; Gaff, S. J.; Gai, M.; Gavalian, G.; Gavrilov, V. B.; Gilad, S.; Gilfoyle, G. P.; Giovanetti, K. L.; Girard, P.; Golovatch, E.; Gordon, C. I.; Griffioen, K. A.; Guidal, M.; Guillo, M.; Guo, L.; Gyurjyan, V.; Hadjidakis, C.; Hancock, D.; Hardie, J.; Heddle, D.; Heimberg, P.; Hersman, F. W.; Hicks, K.; Hicks, R. S.; Holtrop, M.; Hu, J.; Hyde-Wright, C. E.; Ito, M. M.; Jenkins, D.; Joo, K.; Keith, C.; Kelley, J. H.; Khandaker, M.; Kim, K. Y.; Kim, K.; Kim, W.; Klein, A.; Klein, F. J.; Klimenko, A. V.; Klusman, M.; Kossov, M.; Kramer, L. H.; Kuang, Y.; Kuhn, J.; Lachniet, J.; Laget, J. M.; Lawrence, D.; Leksin, G. A.; Loukachine, K.; Major, R. W.; Manak, J. J.; Marchand, C.; McAleer, S.; McNabb, J. W.; McCarthy, J.; Mecking, B. A.; Mestayer, M. D.; Meyer, C. A.; Minehart, R.; Mirazita, M.; Miskimen, R.; Mokeev, V.; Morrow, S.; Muccifora, V.; Mueller, J.; Murphy, L. Y.; Mutchler, G. S.; Napolitano, J.; Nelson, S. O.; Niccolai, S.; Niculescu, G.; Niczyporuk, B.; Niyazov, R. A.; Nozar, M.; O'Rielly, G. V.; Ohandjanyan, M. S.; Opper, A.; Ossipenko, M.; Park, K.; Patois, Y.; Peterson, G. A.; Philips, S.; Pivnyuk, N.; Pocanic, D.; Pogorelko, O.; Polli, E.; Preedom, B. M.; Price, J. W.; Protopopescu, D.; Qin, L. M.; Raue, B. A.; Riccardi, G.; Ricco, G.; Ripani, M.; Ritchie, B. G.; Rock, S.; Ronchetti, F.; Rossi, P.; Rowntree, D.; Rubin, P. D.; Sabourov, K.; Salgado, C. W.; Sapunenko, V.; Sargsyan, M.; Schumacher, R. A.; Serov, V. S.; Sharabian, Y. G.; Shaw, J.; Shuvalov, S. M.; Simionatto, S.; Skabelin, A.; Smith, E. S.; Smith, L. C.; Smith, T.; Sober, D. I.; Sorrell, L.; Spraker, M.; Stepanyan, S.; Stoler, P.; Taylor, S.; Tedeschi, D.; Thoma, U.; Thompson, R.; Todor, L.; Tung, T. Y.; Tur, C.; Vineyard, M. F.; Vlassov, A.; Wang, K.; Weinstein, L. B.; Weller, H.; Welsh, R.; Weygand, D. P.; Whisnant, S.; Witkowski, M.; Wolin, E.; Wood, M. H.; Yegneswaran, A.; Zhang, B.; Zhao, J.; Zhou, Z.

    2003-05-01

    We report the results of a new measurement of spin structure functions of the deuteron in the region of moderate momentum transfer [Q2=0.27 1.3 (GeV/c)2] and final hadronic state mass in the nucleon resonance region (W=1.08 2.0 GeV). We scattered a 2.5 GeV polarized continuous electron beam at Jefferson Lab off a dynamically polarized cryogenic solid state target (15ND3) and detected the scattered electrons with the CEBAF large acceptance spectrometer. From our data, we extract the longitudinal double spin asymmetry A|| and the spin structure function gd1. Our data are generally in reasonable agreement with existing data from SLAC where they overlap, and they represent a substantial improvement in statistical precision. We compare our results with expectations for resonance asymmetries and extrapolated deep inelastic scaling results. Finally, we evaluate the first moment of the structure function gd1 and study its approach to both the deep inelastic limit at large Q2 and to the Gerasimov-Drell-Hearn sum rule at the real photon limit (Q2→0). We find that the first moment varies rapidly in the Q2 range of our experiment and crosses zero at Q2 between 0.5 and 0.8 (GeV/c)2, indicating the importance of the Δ resonance at these momentum transfers.

  8. Structure, function, and genetics of lipoprotein (a).

    PubMed

    Schmidt, Konrad; Noureen, Asma; Kronenberg, Florian; Utermann, Gerd

    2016-08-01

    Lipoprotein (a) [Lp(a)] has attracted the interest of researchers and physicians due to its intriguing properties, including an intragenic multiallelic copy number variation in the LPA gene and the strong association with coronary heart disease (CHD). This review summarizes present knowledge of the structure, function, and genetics of Lp(a) with emphasis on the molecular and population genetics of the Lp(a)/LPA trait, as well as aspects of genetic epidemiology. It highlights the role of genetics in establishing Lp(a) as a risk factor for CHD, but also discusses uncertainties, controversies, and lack of knowledge on several aspects of the genetic Lp(a) trait, not least its function. PMID:27074913

  9. The Spin Structure Function g2

    SciTech Connect

    Rock, Stephen E.

    2003-02-27

    We have measured the spin structure functions g{sub 2}{sup p} and g{sub 2}{sup d} over the kinematic range 0.02 {le} x {le} 0.8 and 0.7 {le} Q{sup 2} {le} 20 GeV{sup 2} by scattering 29.1 and 32.3 GeV longitudinally polarized electrons from transversely polarized NH{sub 3} and {sup 6}LiD targets. Our measured g{sub 2} approximately follows the twist-2 Wandzura-Wilczek calculation. The twist-3 reduced matrix elements d{sub 2}{sup p} and d{sub 2}{sup n} are less than two standard deviations from zero. The data are inconsistent with the Burkhardt-Cottingham sum rule. The Efremov-Leader-Teryaev integral is consistent with zero within our measured kinematic range.

  10. Structure-function correlations in tyrosinases.

    PubMed

    Kanteev, Margarita; Goldfeder, Mor; Fishman, Ayelet

    2015-09-01

    Tyrosinases are metalloenzymes belonging to the type-3 copper protein family which contain two copper ions in the active site. They are found in various prokaryotes as well as in plants, fungi, arthropods, and mammals and are responsible for pigmentation, wound healing, radiation protection, and primary immune response. Tyrosinases perform two sequential enzymatic reactions: hydroxylation of monophenols and oxidation of diphenols to form quinones which polymerize spontaneously to melanin. Two other members of this family are catechol oxidases, which are prevalent mainly in plants and perform only the second oxidation step, and hemocyanins, which lack enzymatic activity and are oxygen carriers. In the last decade, several structures of plant and bacterial tyrosinases were determined, some with substrates or inhibitors, highlighting features and residues which are important for copper uptake and catalysis. This review summarizes the updated information on structure-function correlations in tyrosinases along with comparison to other type-3 copper proteins. PMID:26104241

  11. Structure, Function and Regulation of the Clostridium cellulovorans Cellulosome

    SciTech Connect

    Doi, Roy H

    2008-06-01

    Our major goal for this project (2004-2008) was to obtain an understanding ofthe structure, function, and regulation of the Clostridium cellulovorans cellulosomes. Our specific goals were to select genes for cellulosomal and non-cellulosomal enzymes and characterize their products, to study the synergistic action between cellulosomal and non-cellulosomal enzymes, to study the composition of cellulosomes when cells were grown with different carbon sources, continue our studies on the scaffolding protein and examine heterologous expression of cellulosomal genes in Bacillus subtilis. We fulfilled the specific goals of our proposal.

  12. In Situ TEM Nanoindentation Studies on Stress-Induced Phase Transformations in Metallic Materials

    NASA Astrophysics Data System (ADS)

    Liu, Y.; Wang, H.; Zhang, X.

    2016-01-01

    Although abundant phase transformations are in general thermally driven processes, there are many examples wherein stresses can induce phase transformations. Numerous in situ techniques, such as in situ x-ray diffraction and neutron diffraction, have been applied to reveal phase transformations. Recently, an in situ nanoindentation technique coupled with transmission electron microscopy demonstrated the capability to directly correlating stresses with phase transformations and microstructural evolutions at a submicron length scale. Here we briefly review in situ studies on stress-induced diffusional and diffusionless phase transformations in amorphous CuZrAl alloy and NiFeGa shape memory alloy. In the amorphous CuZrAl, in situ nanoindentation studies show that the nucleation of nanocrystals (a diffusional process) occurs at ultra-low stresses manifested by a prominent stress drop. In the NiFeGa shape memory alloy, two distinctive types of martensitic (diffusionless) phase transformations accompanied by stress plateaus are observed, including a reversible gradual phase transformation at low stress levels, and an irreversible abrupt phase transition at higher stress levels.

  13. Microcosm and in situ field studies of enhanced biotransformation of trichloroethylene by phenol-utilizing microorganisms.

    PubMed Central

    Hopkins, G D; Semprini, L; McCarty, P L

    1993-01-01

    The ability of different aerobic groundwater microorganisms to cometabolically degrade trichloroethylene (TCE), 1,2-cis-dichloroethylene (c-DCE), and 1,2-trans-dichloroethylene (t-DCE) was evaluated both in groundwater-fed microcosms and in situ in a shallow aquifer. Microcosms amended with phenol or toulene were equally effective in removing c-DCE (> 90%) followed by TCE (60 to 70%), while the microcosm fed methane was most effective in removing t-DCE (> 90%). The microcosm fed ammonia was the least effective. None of the microcosms effectively degraded 1,1,1-trichloroethane. At the Moffett Field groundwater test site, in situ removal of c-DCE and TCE coincided with biostimulation through phenol and oxygen injection and utilization, with c-DCE removed more rapidly than TCE. Greater TCE and c-DCE removal was observed when the phenol concentration was increased. Over 90% removal of c-DCE and TCE was observed in the 2-m biostimulated zone. This compares with 40 to 50% removal of c-DCE and 15 to 25% removal of TCE achieved by methane-grown microorganisms previously evaluated in an adjacent in situ test zone. The in situ removal with phenol-grown microorganisms agrees qualitatively with the microcosm studies, with the rates and extents of removal ranked as follows: c-DCE > TCE > t-DCE. These studies demonstrate the potential for in situ TCE bioremediation using microorganisms grown on phenol. PMID:8357259

  14. In Situ TEM Nanoindentation Studies on Stress-Induced Phase Transformations in Metallic Materials

    DOE PAGESBeta

    Liu, Y.; Wang, H.; Zhang, X.

    2015-11-30

    Though abundant phase transformations are in general thermally driven processes, there are many examples wherein stresses can induce phase transformations. We applied numerous in situ techniques, such as in situ x-ray diffraction and neutron diffraction in order to reveal phase transformations. Recently, an in situ nanoindentation technique coupled with transmission electron microscopy demonstrated the capability to directly correlating stresses with phase transformations and microstructural evolutions at a submicron length scale. We briefly review in situ studies on stress-induced diffusional and diffusionless phase transformations in amorphous CuZrAl alloy and NiFeGa shape memory alloy. Moreover, in the amorphous CuZrAl, in situ nanoindentationmore » studies show that the nucleation of nanocrystals (a diffusional process) occurs at ultra-low stresses manifested by a prominent stress drop. In the NiFeGa shape memory alloy, two distinctive types of martensitic (diffusionless) phase transformations accompanied by stress plateaus are observed, including a reversible gradual phase transformation at low stress levels, and an irreversible abrupt phase transition at higher stress levels.« less

  15. In Situ TEM Nanoindentation Studies on Stress-Induced Phase Transformations in Metallic Materials

    SciTech Connect

    Liu, Y.; Wang, H.; Zhang, X.

    2015-11-30

    Though abundant phase transformations are in general thermally driven processes, there are many examples wherein stresses can induce phase transformations. We applied numerous in situ techniques, such as in situ x-ray diffraction and neutron diffraction in order to reveal phase transformations. Recently, an in situ nanoindentation technique coupled with transmission electron microscopy demonstrated the capability to directly correlating stresses with phase transformations and microstructural evolutions at a submicron length scale. We briefly review in situ studies on stress-induced diffusional and diffusionless phase transformations in amorphous CuZrAl alloy and NiFeGa shape memory alloy. Moreover, in the amorphous CuZrAl, in situ nanoindentation studies show that the nucleation of nanocrystals (a diffusional process) occurs at ultra-low stresses manifested by a prominent stress drop. In the NiFeGa shape memory alloy, two distinctive types of martensitic (diffusionless) phase transformations accompanied by stress plateaus are observed, including a reversible gradual phase transformation at low stress levels, and an irreversible abrupt phase transition at higher stress levels.

  16. In situ studies of mass transport in liquid alloys by means of neutron radiography.

    PubMed

    Kargl, F; Engelhardt, M; Yang, F; Weis, H; Schmakat, P; Schillinger, B; Griesche, A; Meyer, A

    2011-06-29

    When in situ techniques became available in recent years this led to a breakthrough in accurately determining diffusion coefficients for liquid alloys. Here we discuss how neutron radiography can be used to measure chemical diffusion in a ternary AlCuAg alloy. Neutron radiography hereby gives complementary information to x-ray radiography used for measuring chemical diffusion and to quasielastic neutron scattering used mainly for determining self-diffusion. A novel Al(2)O(3) based furnace that enables one to study diffusion processes by means of neutron radiography is discussed. A chemical diffusion coefficient of Ag against Al around the eutectic composition Al(68.6)Cu(13.8)Ag(17.6) at.% was obtained. It is demonstrated that the in situ technique of neutron radiography is a powerful means to study mass transport properties in situ in binary and ternary alloys that show poor x-ray contrast. PMID:21654050

  17. Structure Function for High-Concentration Biophantoms of Polydisperse Scatterer Sizes

    PubMed Central

    Han, Aiguo; O’Brien, William D.

    2015-01-01

    Ultrasonic backscattering coefficient (BSC) has been used extensively to characterize tissue. In most cases, sparse scatterer concentrations are assumed. However, many types of tissues have dense scattering media. This study addresses the problem of dense media scattering by taking into account the correlation among scatterers using the structure functions. The effect of scatterer polydispersity on the structure functions is investigated. Structure function models based on polydisperse scatterers are theoretically developed and experimentally evaluated against the structure functions obtained from cell pellet biophantoms. The biophantoms were constructed by placing live cells of known concentration in coagulation media to form a clot. The BSCs of the biophantoms were estimated using single-element transducers over the frequency range from 11 to 105 MHz. Experimental structure functions were obtained by comparing the BSCs of two cell concentrations. The structure functions predicted by the models agreed with the experimental structure functions. Fitting the models yielded cell radius estimates that were consistent with direct light microscope measures. The results demonstrate the role of scatterer position correlation on dense media scattering, and the significance of scatterer polydispersity on structure functions. This work may lead to more accurate modeling of ultrasonic scattering in dense medium for improved tissue characterization. PMID:25643080

  18. Antimicrobial effect of chlorhexidine digluconate in dentin: In vitro and in situ study

    PubMed Central

    Borges, Fátima Maria Cavalcante; de Melo, Mary Anne Sampaio; Lima, Juliana Paiva Marques; Zanin, Iriana Carla Junqueria; Rodrigues, Lidiany Karla Azevedo

    2012-01-01

    Aim: The aim of this study was to evaluate a very short-term in vitro and in situ effect of 2% chlorhexidine-digluconate-based (CHX) cavity cleanser on the disinfection of dentin demineralized by cariogenic bacteria. Materials and Methods: Human dentin slabs were randomly allocated and used in 2 distinct phases, in vitro and in situ, for obtaining demineralized dentin. In vitro, the slabs (n=15) were immersed for 5 days in BHI broth inoculated with Streptococcus mutans CTT 3440. In situ, a double-blind design was conducted in one phase of 14 days, during which 20 volunteers wore palatal devices containing two human dental dentin slabs. On 5th day in vitro and 14th day in situ, the slabs were allocated to the two groups: Control group (5 μl of 0.9% NaCl solution) and CHX group (5 μl of 2% chlorhexidine digluconate solution, Cavity Cleanser™ BISCO, Schaumburg, IL, EUA), for 5 minutes. The microbiological analyses were performed immediately before and after the treatments. Results: The log reductions means found for CHX treatment on tested micro organisms were higher when compared to Control group either in vitro or in situ conditions. Conclusions: Our results showed that CHX was effective in reducing the cultivable microbiota in contaminated dentin. Furthermore, although the use of chlorhexidine-digluconate-based cavity disinfectant did not completely eliminate the viable microorganisms, it served as a suitable agent to disinfect tooth preparations. PMID:22368330

  19. How to design in situ studies: an evaluation of experimental protocols

    PubMed Central

    Sung, Young-Hye; Kim, Hae-Young; Son, Ho-Hyun

    2014-01-01

    Objectives Designing in situ models for caries research is a demanding procedure, as both clinical and laboratory parameters need to be incorporated in a single study. This study aimed to construct an informative guideline for planning in situ models relevant to preexisting caries studies. Materials and Methods An electronic literature search of the PubMed database was performed. A total 191 of full articles written in English were included and data were extracted from materials and methods. Multiple variables were analyzed in relation to the publication types, participant characteristics, specimen and appliance factors, and other conditions. Frequencies and percentages were displayed to summarize the data and the Pearson's chi-square test was used to assess a statistical significance (p < 0.05). Results There were many parameters commonly included in the majority of in situ models such as inclusion criteria, sample sizes, sample allocation methods, tooth types, intraoral appliance types, sterilization methods, study periods, outcome measures, experimental interventions, etc. Interrelationships existed between the main research topics and some parameters (outcome measures and sample allocation methods) among the evaluated articles. Conclusions It will be possible to establish standardized in situ protocols according to the research topics. Furthermore, data collaboration from comparable studies would be enhanced by homogeneous study designs. PMID:25110639

  20. In-situ study of interconnect failures by electromigration inside a scanning electron microscope

    NASA Astrophysics Data System (ADS)

    Wetzig, Klaus; Wendrock, Horst; Buerke, Axel; Kötter, Thomas

    1999-11-01

    The influence of microstructure on electromigration damage of Al and Cu interconnects with different width and morphology was studied. At first, grain boundaries and local grain orientations before electromigration were registered and correlated with defect places. The investigations focussed on in-situ electromigration tests inside a SEM under accelerated loading conditions, on the in-situ observation of defect formation, and on orientation measurements at the interconnect grains. The position of individual grain boundaries and the misorientation of their neighbored grains seem to be decisive factors for the interconnect failure because of different diffusivities. Whereas the failure behavior of polycrystalline interconnects is sufficiently understood, bamboo structures require further investigations.

  1. Preparation of multilayered materials in cross-section for in situ TEM tensile deformation studies

    SciTech Connect

    Wall, M. A., LLNL

    1997-05-13

    The success of in-situ transmission electron microscopy experimentation is often dictated by proper specimen preparation. We report here a novel technique permitting the production of cross-sectioned tensile specimens of multilayered films for in-situ deformation studies. Of primary importance in the development of this technique is the production of an electron transparent micro-gauge section using focused ion beam technology. This microgauge section predetermines the position at which plastic deformation is initiated; crack nucleation, growth and failure are then subsequently observed.

  2. Study of in-situ degradation of thermal control surfaces

    NASA Technical Reports Server (NTRS)

    Gilligan, J. E.; Zerlaut, G. A.

    1972-01-01

    Experimental technique used in study of damage mechanism to semiconductor pigments exposed to ultraviolet radiation can be adapted for investigations of surface chemistry and may be used analytically to determine contamination.

  3. Development of in situ respirometers for ocean acidification studies

    NASA Astrophysics Data System (ADS)

    Risi, M. A.; Barry, J. P.; Buck, K. R.; Okuda, C. M.; Reisenbichler, K. R.; Robison, B. H.

    2009-12-01

    Studies of metabolic rates of deep-sea organisms are important components of research addressing the biological impacts of ocean acidification. These studies contribute to our understanding of the ocean carbon cycle by identifying the pathways and rates of organic carbon fluxes in ocean ecosystems. Oxygen consumption is expected to decrease in most animals in response to hypercapnic (high-CO2) stress, due to disruption of internal acid/base balance. To perform these field and laboratory studies, a respirometry system utilizing a controller with a distributed architecture was developed. The architecture has allowed the system to be adapted to midwater and benthic respirometers. The distributed nature of the architecture allows the easy expansion of the respirometers as well as the integration of new sensors. An overview of the system and field results to date will be presented.

  4. In situ and ex situ XANES study of nanodispersed Mo species in zeolites used in fine chemistry catalysis.

    PubMed

    Rentería, M; Traverse, A; Anunziata, O A; Lede, E J; Pierella, L; Requejo, F G

    2001-03-01

    Mo K-edge XANES experiments on Mo-containing zeolites at low Mo loading (1 and 2 wt% of Mo on H-ZSM-11, H-BETA and H-ZSM-5 catalysts), active in fine chemistry reactions, were performed ex situ as function of sample calcination temperature in air (in the range 773-973 K) or in situ at 873 and 973K under N2 flow. The results showed a 4-fold oxygen coordination for the incorporated Mo species in the activated (dehydrated) state. Combining these results with additional data evidences an almost total Mo exchange inside the zeolite channels. PMID:11512876

  5. In-Situ Chemical Reduction and Oxidation of VOCs in Groundwater: Groundwater Treatability Studies

    NASA Technical Reports Server (NTRS)

    Keith, Amy; Glasgow, Jason; McCaleh, Rececca C. (Technical Monitor)

    2001-01-01

    This paper presents NASA Marshall Space Flight Center's treatability studies for volatile organic compounds in groundwater. In-Situ groundwater treatment technologies include: 1) Chemical Reduction(Ferox); 2) Chemical Oxidation (Fenton Reagents, Permanganate, and Persulfate); and 3) Thermal (Dynamic Underground Stripping, Six-Phase Heating). This paper is presented in viewgraph form.

  6. In Situ Transmission Electron Microscopy Heating Studies of Particle Coalescence and Microstructure Evolution in Nanosized Ceramics

    SciTech Connect

    2006-06-02

    Final report on in-situ transmission microscopy heating studies of particle coalescence and microstructure evolution in nanosized ceramics. Report includes summary of work on particle shape changes and stress effects, and novel infiltration techniques in the processing of alumina based ceramics.

  7. In situ fixation of lead in soil: A case study

    SciTech Connect

    Keefe, M.; Robinson, W.W.

    1995-12-31

    Excavation and treatment of lead contaminated soil is routine today. Much less typical is the case where the soil is remediated and placed back into immediate use through the application of insitue techniques. A case study will be presented that will highlight the problem and the unique problem solving approach that allowed the site owner to promptly return his property to productive use.

  8. An in situ sample environment reaction cell for spatially resolved x-ray absorption spectroscopy studies of powders and small structured reactors

    NASA Astrophysics Data System (ADS)

    Zhang, Chu; Gustafson, Johan; Merte, Lindsay R.; Evertsson, Jonas; Norén, Katarina; Carlson, Stefan; Svensson, Hâkan; Carlsson, Per-Anders

    2015-03-01

    An easy-to-use sample environment reaction cell for X-ray based in situ studies of powders and small structured samples, e.g., powder, pellet, and monolith catalysts, is described. The design of the cell allows for flexible use of appropriate X-ray transparent windows, shielding the sample from ambient conditions, such that incident X-ray energies as low as 3 keV can be used. Thus, in situ X-ray absorption spectroscopy (XAS) measurements in either transmission or fluorescence mode are facilitated. Total gas flows up to about 500 mln/min can be fed while the sample temperature is accurately controlled (at least) in the range of 25-500 °C. The gas feed is composed by a versatile gas-mixing system and the effluent gas flow composition is monitored with mass spectrometry (MS). These systems are described briefly. Results from simultaneous XAS/MS measurements during oxidation of carbon monoxide over a 4% Pt/Al2O3 powder catalyst are used to illustrate the system performance in terms of transmission XAS. Also, 2.2% Pd/Al2O3 and 2% Ag - Al2O3 powder catalysts have been used to demonstrate X-ray absorption near-edge structure (XANES) spectroscopy in fluorescence mode. Further, a 2% Pt/Al2O3 monolith catalyst was used ex situ for transmission XANES. The reaction cell opens for facile studies of structure-function relationships for model as well as realistic catalysts both in the form of powders, small pellets, and coated or extruded monoliths at near realistic conditions. The applicability of the cell for X-ray diffraction measurements is discussed.

  9. An in situ sample environment reaction cell for spatially resolved x-ray absorption spectroscopy studies of powders and small structured reactors

    SciTech Connect

    Zhang, Chu; Gustafson, Johan; Merte, Lindsay R.; Evertsson, Jonas; Norén, Katarina; Carlson, Stefan; Svensson, Håkan; Carlsson, Per-Anders

    2015-03-15

    An easy-to-use sample environment reaction cell for X-ray based in situ studies of powders and small structured samples, e.g., powder, pellet, and monolith catalysts, is described. The design of the cell allows for flexible use of appropriate X-ray transparent windows, shielding the sample from ambient conditions, such that incident X-ray energies as low as 3 keV can be used. Thus, in situ X-ray absorption spectroscopy (XAS) measurements in either transmission or fluorescence mode are facilitated. Total gas flows up to about 500 ml{sub n}/min can be fed while the sample temperature is accurately controlled (at least) in the range of 25–500 °C. The gas feed is composed by a versatile gas-mixing system and the effluent gas flow composition is monitored with mass spectrometry (MS). These systems are described briefly. Results from simultaneous XAS/MS measurements during oxidation of carbon monoxide over a 4% Pt/Al{sub 2}O{sub 3} powder catalyst are used to illustrate the system performance in terms of transmission XAS. Also, 2.2% Pd/Al{sub 2}O{sub 3} and 2% Ag − Al{sub 2}O{sub 3} powder catalysts have been used to demonstrate X-ray absorption near-edge structure (XANES) spectroscopy in fluorescence mode. Further, a 2% Pt/Al{sub 2}O{sub 3} monolith catalyst was used ex situ for transmission XANES. The reaction cell opens for facile studies of structure-function relationships for model as well as realistic catalysts both in the form of powders, small pellets, and coated or extruded monoliths at near realistic conditions. The applicability of the cell for X-ray diffraction measurements is discussed.

  10. A New Mixed Model Based on the Velocity Structure Function

    NASA Astrophysics Data System (ADS)

    Brun, Christophe; Friedrich, Rainer; Da Silva, Carlos B.; Métais, Olivier

    We propose a new mixed model for Large Eddy-Simulation based on the 3D spatial velocity increment. This approach blends the non-linear properties of the Increment model (Brun & Friedrich (2001)) with the eddy viscosity characteristics of the Structure Function model (Métais & Lesieur (1992)). The behaviour of this subgrid scale model is studied both via a priori tests of a plane jet at ReH=3000 and Large Eddy-Simulation of a round jet at ReD=25000. This approach allows to describe both forward and backward energy transfer encountered in transitional shear flows.

  11. Combined in situ XRD and in situ XANES studies on the reduction behavior of a rhenium promoted cobalt catalyst.

    PubMed

    Kumar, Nitin; Payzant, E A; Jothimurugesan, K; Spivey, J J

    2011-08-28

    A 10% Co-4% Re/(2% Zr/SiO(2)) catalyst was prepared by co-impregnation using a silica support modified by 2% Zr. The catalyst was characterized by temperature programmed reduction (TPR), in situ XRD and in situ XANES analysis where it was simultaneously exposed to H(2) using a temperature programmed ramp. The results showed the two step reduction of large crystalline Co(3)O(4) with CoO as an intermediate. TPR results showed that the reduction of highly dispersed Co(3)O(4) was facilitated by reduced rhenium by a H(2)-spillover mechanism. In situ XRD results showed the presence of both, Co-hcp and Co-fcc phases in the reduced catalyst at 400 °C. However, the Co-hcp phase was more abundant, which is thought to be the more active phase as compared to the Co-fcc phase for CO hydrogenation. CO hydrogenation at 270 °C and 5 bar pressure produces no detectable change in the phases during the time of experiment. In situ XANES results showed a decrease in the metallic cobalt in the presence of H(2)/CO, which can be attributed due to oxidation of the catalyst by reaction under these conditions. PMID:21743918

  12. IN SITU INFRARED STUDY OF CATALYTIC DECOMPOSITION OF NO

    SciTech Connect

    KHALID ALMUSAITEER; RAM KRISHNAMURTHY; STEVEN S.C. CHUANG

    1998-08-18

    The growing concerns for the environment and increasingly stringent standards for NO emission have presented a major challenge to control NO emissions from electric utility plants and automobiles. Catalytic decomposition of NO is the most attractive approach for the control of NO emission for its simplicity. Successful development of an effective catalyst for NO decomposition will greatly decrease the equipment and operation cost of NO control. Due to lack of understanding of the mechanism of NO decomposition, efforts on the search of an effective catalyst have been unsuccessful. Scientific development of an effective catalyst requires fundamental understanding of the nature of active site, the rate-limiting step, and an approach to prolong the life of the catalyst. Research is proposed to study the reactivity of adsorbates for the direct NO decomposition and to investigate the feasibility of two novel approaches for improving catalyst activity and resistance to sintering. The first approach is the use of silanation to stabilize metal crystallites and supports for Cu-ZSM-5 and promoted Pt catalysts; the second is utilization of oxygen spillover and desorption to enhance NO decomposition activity. An innovative infrared reactor system will be used to observe and determine the dynamic behavior and the reactivity of adsorbates during NO decomposition, oxygen spillover, and silanation. A series of experiments including X-ray diffraction, temperature programmed desorption, temperature programmed reaction, X-ray photoelectron spectroscopy will be used to characterized the catalysts. The information obtained from this study will provide a scientific basis for developing an effective catalyst for the NO decomposition under practical flue gas conditions.

  13. In Situ Infrared Study of Catalytic Decomposition of NO

    SciTech Connect

    Cher-Dip Tan; Steven S.C. Chuang

    1997-07-17

    The growing concerns for the environment and increasingly stringent standards for NO emission have presented a major challenge to control NO emmissions from electric utility plants and automobiles. Catalytic decomposition of NO is the most attractive approach for the control of NO emission for its simplicity. Successful development of an effective catalyst for NO decomposition will greatly decrease the equipment and operation cost of NO control. Due to lack of understanding of the mechanism of NO decomposition, efforts on the search of an effective catalyst have been unsuccesful. Scientific development of an effective catalyst requires fundamental understanding of the nature of active site, the rate-limiting step, and an approach to prolong the life of the catalyst. Research is proposed to study the reactivity of adsorbates for the direct NO decomposition and to investigate the feasibility of two novel approaches for improving catalyst activity and resistance to sintering. The first approach is the use of silanation to stabilize metal crystallites and supports for Cu-ZSM-5 and promoted Pt catalysts; the second is utilization of oxygen spillover and desorption to enhance NO decomposition activity. An innovative infrared reactor system will be used to observe and determine the dynamic behavior and the reactivity of adsorbates during NO decomposition, oxygen spillover, and silanation. A series of experiments including X-ray diffraction, temperature programmed desorption, temperature programmed reaction, X-ray photoelectron spectroscopy will be used to characterized the catalysts. The information obtained from this study will provide a scientific basis for developing an effective catalyst for the NO decomposition under practical flue gas conditions.

  14. Cost studies of thermally enhanced in situ soil remediation technologies

    SciTech Connect

    Bremser, J.; Booth, S.R.

    1996-05-01

    This report describes five thermally enhanced technologies that may be used to remediate contaminated soil and water resources. The standard methods of treating these contaminated areas are Soil Vapor Extraction (SVE), Excavate & Treat (E&T), and Pump & Treat (P&T). Depending on the conditions at a given site, one or more of these conventional alternatives may be employed; however, several new thermally enhanced technologies for soil decontamination are emerging. These technologies are still in demonstration programs which generally are showing great success at achieving the expected remediation results. The cost savings reported in this work assume that the technologies will ultimately perform as anticipated by their developers in a normal environmental restoration work environment. The five technologies analyzed in this report are Low Frequency Heating (LF or Ohmic, both 3 and 6 phase AC), Dynamic Underground Stripping (DUS), Radio Frequency Heating (RF), Radio Frequency Heating using Dipole Antennae (RFD), and Thermally Enhanced Vapor Extraction System (TEVES). In all of these technologies the introduction of heat to the formation raises vapor pressures accelerating contaminant evaporation rates and increases soil permeability raising diffusion rates of contaminants. The physical process enhancements resulting from temperature elevations permit a greater percentage of volatile organic compound (VOC) or semi- volatile organic compound (SVOC) contaminants to be driven out of the soils for treatment or capture in a much shorter time period. This report presents the results of cost-comparative studies between these new thermally enhanced technologies and the conventional technologies, as applied to five specific scenarios.

  15. In situ dynamic study of hydrogen oxidation on rhodium.

    PubMed

    Visart de Bacarmé, T; Bär, T; Kruse, N

    2001-10-01

    The reaction of hydrogen/oxygen gas mixtures with rhodium single crystals was studied using video-FIM (Field Ion Microscopy) at temperatures between 350 and 550 K and up to 2 x 10(-2) Pa total pressure. Imaging at 500 K in a hydrogen rich gas mixture (H2:O2 = 9) revealed considerable morphological changes of the (0 0 1)-oriented field emitter tip, i.e. the growth of low-index at the expense of high-index planes and strong crystal coarsening. Decreasing the hydrogen partial pressure led to chemical and structural changes of the Rh sample. Starting on the [1 1 0] planes a surface oxide formed, which spread anisotropically across the surface until it finally covered the whole visible surface area. The transformation was reversible upon increasing the hydrogen pressure back to its initial value. However, a hysteresis behavior was observed, i.e. a larger hydrogen partial pressure was found to be necessary to re-establish the initial patterns of a reactive Oad/Had layer. By varying the temperature from 400 to 500 K a phase diagram was established for the Oad/Had system. Increasing the electric field proved to shift the phase diagram towards higher H2 pressures. At 550K self-sustained kinetic oscillations with a cycle time of approximately 40s could be observed. PMID:11770755

  16. Nitric oxide synthases: structure, function and inhibition.

    PubMed Central

    Alderton, W K; Cooper, C E; Knowles, R G

    2001-01-01

    This review concentrates on advances in nitric oxide synthase (NOS) structure, function and inhibition made in the last seven years, during which time substantial advances have been made in our understanding of this enzyme family. There is now information on the enzyme structure at all levels from primary (amino acid sequence) to quaternary (dimerization, association with other proteins) structure. The crystal structures of the oxygenase domains of inducible NOS (iNOS) and vascular endothelial NOS (eNOS) allow us to interpret other information in the context of this important part of the enzyme, with its binding sites for iron protoporphyrin IX (haem), biopterin, L-arginine, and the many inhibitors which interact with them. The exact nature of the NOS reaction, its mechanism and its products continue to be sources of controversy. The role of the biopterin cofactor is now becoming clearer, with emerging data implicating one-electron redox cycling as well as the multiple allosteric effects on enzyme activity. Regulation of the NOSs has been described at all levels from gene transcription to covalent modification and allosteric regulation of the enzyme itself. A wide range of NOS inhibitors have been discussed, interacting with the enzyme in diverse ways in terms of site and mechanism of inhibition, time-dependence and selectivity for individual isoforms, although there are many pitfalls and misunderstandings of these aspects. Highly selective inhibitors of iNOS versus eNOS and neuronal NOS have been identified and some of these have potential in the treatment of a range of inflammatory and other conditions in which iNOS has been implicated. PMID:11463332

  17. The ratio of the beauty structure functions Rb=FLb/F2b at low x

    NASA Astrophysics Data System (ADS)

    Boroun, G. R.

    2014-07-01

    We study the structure functions Fkb(x,Q2) (k=2,L) and the reduced cross section σrb(x,Q2) for small values of Bjorken's x variable with respect to the hard (Lipatov) pomeron for the gluon distribution and provide a compact formula for the ratio Rb that is useful to extract the beauty structure function from the beauty reduced cross section, in particular at DESY HERA. Also we show that the effects of the nonlinear corrections to the gluon distribution tame the behavior of the beauty structure function and the beauty reduced cross section at low x.

  18. Structure Function Analysis of AGN Variability using Kepler

    NASA Astrophysics Data System (ADS)

    Kasliwal, Vishal P.; Vogeley, Michael S.; Richards, Gordon T.

    2014-06-01

    We study the variability properties of AGN light-curves observed by the Kepler satellite. AGN optical fluxes are known to exhibit stochastic variations on time-scales of hours, days, months and years. Previous efforts to characterize the stochastic nature of this variability have been hampered by the lack of high-precision space-based measurements of AGN fluxes with regular cadence. Kepler provides light-curves with a S/N ratio of 10-5 for 87 AGN observed over a period of ~ 3 years with a cadence of once every 30 minutes allowing for a detailed examination of the variability process. We probe AGN variability using the Structure Functions of the light-curves of the Kepler AGN. Monte-Carlo simulations of the structure function are used to fit the observed light-curve to models for the Power Spectral Density. We test various models for the form of the PSD including the damped random walk and the powered exponential models. We show that on the shorter time-scales probed by Kepler data, the damped random walk model fails to adequately characterize AGN variability. We find that the PSD may be better modelled by combination of a steep power law of the form 1/f3 on shorter time-scales, and a more shallow power law of the form 1/f2 on the longer time-scales traditionally probed by ground-based variability studies.

  19. Materials testing for in situ stabilization treatability study of INEEL mixed wastes soils

    SciTech Connect

    Heiser, J.; Fuhrmann, M.

    1997-09-01

    This report describes the contaminant-specific materials testing phase of the In Situ Stabilization Comprehensive Environment Response, Compensation, and Liability Act (CERCLA) Treatability Study (TS). The purpose of materials testing is to measure the effectiveness of grouting agents to stabilize Idaho National Engineering and Environmental Laboratory (INEEL) Acid Pit soils and select a grout material for use in the Cold Test Demonstration and Acid Pit Stabilization Treatability Study within the Subsurface Disposal Area (SDA) at the Radioactive Waste Management Complex (RWMC). Test results will assist the selecting a grout material for the follow-on demonstrations described in Test Plan for the Cold Test Demonstration and Acid Pit Stabilization Phases of the In Situ Stabilization Treatability Study at the Radioactive Waste Management Complex.

  20. Time-resolved in situ Studies of Apatite Formation in Aqueous Solutions

    SciTech Connect

    Borkiewicz, O.; Rakovan, J; Cahill, C

    2010-01-01

    Formation of hydroxylapatite through the precipitation and evolution of calcium phosphate precursor phases under varying conditions of temperature (25-90 C), pH (6.5-9.0), and calcium to phosphorus ratio (1.0, 1.33, 1.5, and 1.67) comparable to those found in many sediments and soils were studied. The products of low-temperature precipitation were analyzed by ex situ X-ray diffraction and SEM, as well as time-resolved in situ synchrotron X-ray diffraction. Rietveld refinement was used for quantitative evaluation of relative abundances during phase evolution. The results of ex situ investigations conducted at ambient temperature and near-neutral pH indicate formation of amorphous calcium phosphate, which over the course of experiments transforms to brushite and ultimately hydroxylapatite. The results of in situ X-ray diffraction experiments suggest a more complex pathway of phase development under the same conditions. Some of the initially formed amorphous calcium phosphate and/or crystalline brushite transformed to octacalcium phosphate. In the later stage of the reactions, octacalcium phosphate transforms quite rapidly to hydroxylapatite. This is accompanied or followed by the transformation of the remaining brushite to monetite. Hydroxylapatite and monetite coexist in the sample throughout the remainder of the experiments. In contrast to the near-neutral pH experiments, the results from ex situ and in situ diffraction investigations performed at higher pH yield similar results. The precipitate formed in the initial stages in both types of experiments was identified as amorphous calcium phosphate, which over the course of the reaction quite rapidly transformed to hydroxylapatite without any apparent intermediate phases. This is the first application of time-resolved in situ synchrotron X-ray diffraction to precipitation reactions in the Ca(OH){sub 2}-H{sub 3}PO{sub 4}-H{sub 2}O system. The results indicate that precursors are likely to occur during the natural or

  1. Understanding structure, function, and mutations in the mitochondrial ATP synthase

    PubMed Central

    Xu, Ting; Pagadala, Vijayakanth; Mueller, David M.

    2015-01-01

    The mitochondrial ATP synthase is a multimeric enzyme complex with an overall molecular weight of about 600,000 Da. The ATP synthase is a molecular motor composed of two separable parts: F1 and Fo. The F1 portion contains the catalytic sites for ATP synthesis and protrudes into the mitochondrial matrix. Fo forms a proton turbine that is embedded in the inner membrane and connected to the rotor of F1. The flux of protons flowing down a potential gradient powers the rotation of the rotor driving the synthesis of ATP. Thus, the flow of protons though Fo is coupled to the synthesis of ATP. This review will discuss the structure/function relationship in the ATP synthase as determined by biochemical, crystallographic, and genetic studies. An emphasis will be placed on linking the structure/function relationship with understanding how disease causing mutations or putative single nucleotide polymorphisms (SNPs) in genes encoding the subunits of the ATP synthase, will affect the function of the enzyme and the health of the individual. The review will start by summarizing the current understanding of the subunit composition of the enzyme and the role of the subunits followed by a discussion on known mutations and their effect on the activity of the ATP synthase. The review will conclude with a summary of mutations in genes encoding subunits of the ATP synthase that are known to be responsible for human disease, and a brief discussion on SNPs. PMID:25938092

  2. In situ STM studies of Sb(111) electrodes in aqueous electrolyte solutions

    NASA Astrophysics Data System (ADS)

    Grozovski, V.; Kallip, S.; Lust, E.

    2013-07-01

    The in situ STM studies of Sb(111), which was cleaved at the temperature of liquid nitrogen inside the glove box, and of Sb(111), which was electrochemically polished in the KI + HCl aqueous solution, have been performed under negative polarizations from - 0.8 to - 0.15 V (versus Ag|AgCl in sat. KCl aqueous solution) in the 0.5 M Na2SO4 + 0.0003 M H2SO4 aqueous solution. The atomic resolution has been achieved. The in situ STM data show that there are no quick surface reconstruction processes and the surface structure of cleaved and electrochemically polished Sb(111) is stable within the potential region investigated, similarly for Bi(111) single crystal electrode, previously studied [S. Kallip, E. Lust, Electrochem. Comm. 7 (2005) 863].

  3. In situ electrochemical studies of lithium-ion battery cathodes using atomic force microscopy

    NASA Astrophysics Data System (ADS)

    Ramdon, Sanjay; Bhushan, Bharat; Nagpure, Shrikant C.

    2014-03-01

    Lithium-ion (Li-ion) batteries have been implemented for numerous applications, including plug-in hybrid electric vehicles (PHEV) and pure electric vehicles (EV). In an effort to prolong battery life, it is important to understand the mechanisms that cause reduced battery capacity with aging. Past studies have shown that morphological changes occur in aged cathodes. In situ electrochemical studies using atomic force microscopy allow for the direct observation of the morphology of the Li-ion battery cathode, at a nanometer scale resolution, during the cycling of an electrochemical cell. A simple electrochemical cell designed for in situ characterization is introduced. Charge/discharge curves and morphology data obtained during charging and discharging of cells are presented, and relevant mechanisms are discussed.

  4. Structure-function relationship of monocot mannose-binding lectins.

    PubMed Central

    Barre, A; Van Damme, E J; Peumans, W J; Rougé, P

    1996-01-01

    The monocot mannose-binding lectins are an extended superfamily of structurally and evolutionarily related proteins, which until now have been isolated from species of the Amaryllidaceae, Alliaceae, Araceae, Orchidaceae, and Liliaceae. To explain the obvious differences in biological activities, the structure-function relationships of the monocot mannose-binding lectins were studied by a combination of glycan-binding studies and molecular modeling using the deduced amino acid sequences of the currently known lectins. Molecular modeling indicated that the number of active mannose-binding sites per monomer varies between three and zero. Since the number of binding sites is fairly well correlated with the binding activity measured by surface plasmon resonance, and is also in good agreement with the results of previous studies of the biological activities of the mannose-binding lectins, molecular modeling is of great value for predicting which lectins are best suited for a particular application. PMID:8972598

  5. Feasibility studies of in-situ coal gasification in the Warrior coal field. Quarterly report

    SciTech Connect

    Douglas G.W.; McKinley, M.D.

    1980-01-01

    Studies in support of in-situ gasification involved experiments in bench-scale combustors where three parameters were varied independently: initial fuel bed temperature, applied air flow and water vapor influx rate. Methods for measuring the thermal conductivity of solids at high temperatures were evaluated and measurements of the thermal conductivity and thermal diffusivity were made over a temperature range for several samples of coke. (LTN)

  6. In-situ Studies of Highly Charged Ions at the LLNL EBIT

    SciTech Connect

    Beiersdorfer, P

    2001-08-16

    The properties of highly charged ions and their interaction with electrons and atoms is being studied in-situ at the LLNL electron beam ion traps, EBIT-II and SuperEBIT. Spectroscopic measurements provide data on electron-ion and ion-atom interactions as well as accurate transition energies of lines relevant for understanding QED, nuclear magnetization, and the effects of relativity on complex, state-of-the-art atomic calculations.

  7. Automated data extraction from in situ protein-stable isotope probing studies.

    PubMed

    Slysz, Gordon W; Steinke, Laurey; Ward, David M; Klatt, Christian G; Clauss, Therese R W; Purvine, Samuel O; Payne, Samuel H; Anderson, Gordon A; Smith, Richard D; Lipton, Mary S

    2014-03-01

    Protein-stable isotope probing (protein-SIP) has strong potential for revealing key metabolizing taxa in complex microbial communities. While most protein-SIP work to date has been performed under controlled laboratory conditions to allow extensive isotope labeling of the target organism(s), a key application will be in situ studies of microbial communities for short periods of time under natural conditions that result in small degrees of partial labeling. One hurdle restricting large-scale in situ protein-SIP studies is the lack of algorithms and software for automated data processing of the massive data sets resulting from such studies. In response, we developed Stable Isotope Probing Protein Extraction Resources software (SIPPER) and applied it for large-scale extraction and visualization of data from short-term (3 h) protein-SIP experiments performed in situ on phototrophic bacterial mats isolated from Yellowstone National Park. Several metrics incorporated into the software allow it to support exhaustive analysis of the complex composite isotopic envelope observed as a result of low amounts of partial label incorporation. SIPPER also enables the detection of labeled molecular species without the need for any prior identification. PMID:24467184

  8. Automated data extraction from in situ protein stable isotope probing studies

    SciTech Connect

    Slysz, Gordon W.; Steinke, Laurey A.; Ward, David M.; Klatt, Christian G.; Clauss, Therese RW; Purvine, Samuel O.; Payne, Samuel H.; Anderson, Gordon A.; Smith, Richard D.; Lipton, Mary S.

    2014-01-27

    Protein stable isotope probing (protein-SIP) has strong potential for revealing key metabolizing taxa in complex microbial communities. While most protein-SIP work to date has been performed under controlled laboratory conditions to allow extensive isotope labeling of the target organism, a key application will be in situ studies of microbial communities under conditions that result in small degrees of partial labeling. One hurdle restricting large scale in situ protein-SIP studies is the lack of algorithms and software for automated data processing of the massive data sets resulting from such studies. In response, we developed Stable Isotope Probing Protein Extraction Resources software (SIPPER) and applied it for large scale extraction and visualization of data from short term (3 h) protein-SIP experiments performed in situ on Yellowstone phototrophic bacterial mats. Several metrics incorporated into the software allow it to support exhaustive analysis of the complex composite isotopic envelope observed as a result of low amounts of partial label incorporation. SIPPER also enables the detection of labeled molecular species without the need for any prior identification.

  9. Demonstration testing and evaluation of in situ soil heating. Treatability study work plan, Revision 1

    SciTech Connect

    Sresty, G.C.

    1994-07-07

    A Treatability Study planned for the demonstration of the in situ electromagnetic (EM) heating process to remove organic solvents is described in this Work Plan. The treatability study will be conducted by heating subsurface vadose-zone soils in an organic plume adjacent to the Classified Burial Ground K-1070-D located at K-25 Site, Oak Ridge. The test is scheduled to start during the fourth quarter of FY94 and will be completed during the first quarter of FY95. The EM heating process for soil decontamination is based on volumetric heating technologies developed during the `70s for the recovery of fuels from shale and tar sands by IIT Research Institute (IITRI) under a co-operative program with the US Department of Energy (DOE). Additional modifications of the technology developed during the mid `80s are currently used for the production of heavy oil and waste treatment. Over the last nine years, a number of Government agencies (EPA, Army, AF, and DOE) and industries sponsored further development and testing of the in situ heating and soil decontamination process for the remediation of soils containing hazardous organic contaminants. In this process the soil is heated in situ using electrical energy. The contaminants are removed from the soil due to enhanced vaporization, steam distillation and stripping. IITRI will demonstrate the EM Process for in situ soil decontamination at K-25 Site under the proposed treatability study. Most of the contaminants of concern are volatile organics which can be removed by heating the soil to a temperature range of 85 to 95 C. The efficiency of the treatment will be determined by comparing the concentration of contaminants in soil samples. Samples will be obtained before and after the demonstration for a measurement of the concentration of contaminants of concern.

  10. The human prostacyclin receptor from structure function to disease.

    PubMed

    Martin, Kathleen A; Gleim, Scott; Elderon, Larkin; Fetalvero, Kristina; Hwa, John

    2009-01-01

    Thirty years have passed since Vane and colleagues first described a substance, prostanoid X, from microsomal fractions (later called prostacyclin) that relaxed rather than contracted mesenteric arteries. The critical role of prostacyclin in many pathophysiological conditions, such as atherothrombosis, has only recently become appreciated (through receptor knockout mice studies, selective cyclooxygenase-2 inhibition clinical trials, and the discovery of dysfunctional prostacyclin receptor genetic variants). Additionally, important roles in such diverse areas as pain and inflammation, and parturition are being uncovered. Prostacyclin-based therapies, currently used for pulmonary hypertension, are accordingly emerging as possible treatments for such diseases, fueling interests in structure function studies for the receptor and signal transduction pathways in native cells. The coming decade is likely to yield many further exciting advances. PMID:20374736

  11. Studies of a photochromic model system using NMR with ex-situ and in-situ irradiation devices.

    PubMed

    Wolff, Christiane; Kind, Jonas; Schenderlein, Helge; Bartling, Hanna; Feldmeier, Christian; Gschwind, Ruth M; Biesalski, Markus; Thiele, Christina M

    2016-06-01

    The switching behavior of a photochromic model system was investigated in detail via NMR spectroscopy in order to improve understanding of the compound itself and to provide ways to obtain insights into composition trends of a photo switchable (polymeric) material containing spiropyran/merocyanine units. In addition to the classical irradiation performed outside the magnet (ex-situ), a device for irradiation inside the NMR spectrometer (in-situ) was tested. Both setups are introduced, their advantages and disadvantages as well as their limits are described and the setup for future investigations of photochromic materials is suggested. The influence of different sample concentrations, irradiation procedures, and light intensities on the model system was examined as well as the dependence on solvent, temperature, and irradiation wavelengths. Using the recently published LED illumination device, it was even possible to record two-dimensional spectra on this model system with rather short half-life (7 min in DMSO). This way (13) C chemical shifts of the merocyanine form were obtained, which were unknown before. Copyright © 2016 John Wiley & Sons, Ltd. PMID:26891085

  12. In situ activity recovery of aging biofilm in biological aerated filter: Surfactants treatment and mechanisms study.

    PubMed

    Yu, Qisheng; Huang, Hui; Ren, Hongqiang; Ding, Lili; Geng, Jinju

    2016-11-01

    In situ activity recovery of aging biofilm in the biological aerated filter (BAF) is an important but underappreciated problem. Lab-scaled BAFs were established in this study and three kinds of surfactants containing sodium dodecyl sulfate (SDS), sodium dodecyl benzene sulfonate (SDBS) and rhamnolipid were employed. Multiple indicators including effluent qualities, dissolved organic matters, biofilm physiology and morphology characteristics were investigated to explore the mechanisms. Results showed that removal rates of effluent COD in test groups significantly recovered to the level before aging. Compared with the control, effluent in SDBS and rhamnolipid-treated groups obtained more protein-like and humic-like substances, respectively. Furthermore, great live cell ratio, smooth surface and low adhesion force of biofilm were observed after rhamnolipid treatment, which was in consistent with good effluent qualities in the same group. This is the first report of applying rhamnolipid for in situ activity recovery of aging biofilm in bioreactors. PMID:27513646

  13. Study of dislocations in copper by weak beam, stereo, and in situ straining TEM

    SciTech Connect

    McCabe, R. J.; Misra, A.; Mitchell, T. E.

    2002-01-01

    Conventional transmission electron microscopy (TEM) has been an invaluable tool for verifjhg and developing dislocation theories since the first direct observations of dislocations were made using a TEM in the 1950s. Several useful techniques and technological advancements have been made since, helping fbrther the advancement of dislocation knowledge. The present paper concerns two studies of dislocations in copper made by coupling several of these techniques, specifically weak beam, in situ straining, and stereo TEM. Stereo-TEM coupled with in situ straining TEM was used for tracking 3D dislocation motion and interactions in low dislocation density copper foils. A mechanism by which dislocations in a pileup bypass a dislocation node is observed and discussed. Weak beam TEM is used in conjunction with stereo-TEM to analyze the dislocation content of a dense dislocation wall (DDW).

  14. In Situ Potentiometry and Ellipsometry: A Promising Tool to Study Biofouling of Potentiometric Sensors.

    PubMed

    Lisak, Grzegorz; Arnebrant, Thomas; Lewenstam, Andrzej; Bobacka, Johan; Ruzgas, Tautgirdas

    2016-03-15

    In situ potentiometry and null ellipsometry was combined and used as a tool to follow the kinetics of biofouling of ion-selective electrodes (ISEs). The study was performed using custom-made solid-contact K(+)-ISEs consisting of a gold surface with immobilized 6-(ferrocenyl)hexanethiol as ion-to-electron transducer that was coated with a potassium-selective plasticized polymer membrane. The electrode potential and the ellipsometric signal (corresponding to the amount of adsorbed protein) were recorded simultaneously during adsorption of bovine serum albumin (BSA) at the surface of the K(+)-ISEs. This in situ method may become useful in developing sensors with minimized biofouling. PMID:26864883

  15. Reaction of Formic Acid over Amorphous Manganese Oxide Catalytic Systems: An In Situ Study

    SciTech Connect

    Durand, Jason; Senanayake, Sanjaya D; Mullins, David R; Suib, Steven

    2010-01-01

    The interaction of formic acid with amorphous manganese oxide (AMO) is investigated using in situ photoelectron and infrared spectroscopy techniques. Soft X-ray photoelectron spectroscopy (sXPS) and in situ FTIR illustrate two possible modes of formate bound species at the AMO surface. Two peaks in the IR region from 1340-1390 cm{sup -1} are indicative of formate species bound to the surface in a bidentate configuration. However, a 224 cm{sup -1} band gap between v{sub s}OCO and v{sub as}OCO suggests formate is bound in a bridging configuration. Temperature-programmed desorption studies confirm the formate bound species desorbs as carbon dioxide from the surface at multiple binding sites. At temperatures above 700 K, the presence of K{sup +} {hor_ellipsis} OC complex suggests the bound species interacts at vacant sites related to framework oxygen and cation mobility.

  16. Reaction of Formic Acid over Amorphous Manganese Oxide Catalytic Systems: An In Situ Study

    SciTech Connect

    J Durand; S Senanayake; S Suib; D Mullins

    2011-12-31

    The interaction of formic acid with amorphous manganese oxide (AMO) is investigated using in situ photoelectron and infrared spectroscopy techniques. Soft X-ray photoelectron spectroscopy (sXPS) and in situ FTIR illustrate two possible modes of formate bound species at the AMO surface. Two peaks in the IR region from 1340-1390 cm{sup -1} are indicative of formate species bound to the surface in a bidentate configuration. However, a 224 cm{sup -1} band gap between v{sub s}OCO and v{sub as}OCO suggests formate is bound in a bridging configuration. Temperature-programmed desorption studies confirm the formate bound species desorbs as carbon dioxide from the surface at multiple binding sites. At temperatures above 700 K, the presence of K{sup +} {hor_ellipsis} OC complex suggests the bound species interacts at vacant sites related to framework oxygen and cation mobility.

  17. In situ study of heavy ion irradiation response of immiscible Cu/Fe multilayers

    NASA Astrophysics Data System (ADS)

    Chen, Y.; Li, N.; Bufford, D. C.; Li, J.; Hattar, K.; Wang, H.; Zhang, X.

    2016-07-01

    Recent studies show that immiscible metallic multilayers with incoherent interfaces can effectively reduce defect density in ion irradiated metals by providing active defect sinks that capture and annihilate radiation induced defect clusters. Although it is anticipated that defect density within the layers should vary as a function of distance to the layer interface, there is, to date, little in situ TEM evidence to validate this hypothesis. In this study monolithic Cu films and Cu/Fe multilayers with individual layer thickness, h, of 100 and 5 nm were subjected to in situ Cu ion irradiation at room temperature to nominally 1 displacement-per-atom inside a transmission electron microscope. Rapid formation and propagation of defect clusters were observed in monolithic Cu, whereas fewer defects with smaller dimensions were generated in Cu/Fe multilayers with smaller h. Furthermore in situ video shows that the cumulative defect density in Cu/Fe 100 nm multilayers indeed varies, as a function of distance to the layer interfaces, supporting a long postulated hypothesis.

  18. Development of an in Situ NMR Photoreactor To Study Environmental Photochemistry.

    PubMed

    Bliumkin, Liora; Dutta Majumdar, Rudraksha; Soong, Ronald; Adamo, Antonio; Abbatt, Jonathan P D; Zhao, Ran; Reiner, Eric; Simpson, André J

    2016-06-01

    Photochemistry is a key environmental process directly linked to the fate, source, and toxicity of pollutants in the environment. This study explores two approaches for integrating light sources with nuclear magnetic resonance (NMR) spectroscopy: sample irradiation using a "sunlight simulator" outside the magnet versus direct irradiation of the sample inside the magnet. To assess their applicability, the in situ NMR photoreactors were applied to a series of environmental systems: an atmospheric pollutant (p-nitrophenol), crude oil extracts, and groundwater. The study successfully illustrates that environmentally relevant aqueous photochemical processes can be monitored in situ and in real time using NMR spectroscopy. A range of intermediates and degradation products were identified and matched to the literature. Preliminary measurements of half-lives were also obtained from kinetic curves. The sunlight simulator was shown to be the most suitable model to explore environmental photolytic processes in situ. Other light sources with more intense UV output hold potential for evaluating UV as a remediation alternative in areas such as wastewater treatment plants or oil spills. Finally, the ability to analyze the photolytic fate of trace chemicals at natural abundance in groundwater, using a cryogenic probe, demonstrates the viability of NMR spectroscopy as a powerful and complementary technique for environmental applications in general. PMID:27172272

  19. In Situ Transmission Electron Microscopy And Spectroscopy Studies Of Rechargeable Batteries Under Dynamic Operating Conditions: A Retrospective And Perspective View

    SciTech Connect

    Wang, Chong M.

    2015-02-14

    Since the advent of the transmission electron microscope (TEM), continuing efforts have been made to image material under native and reaction environments that typically involve liquids, gases, and external stimuli. With the advances of aberration-corrected TEM for improving the imaging resolution, steady progress has been made on developing methodologies that allow imaging under dynamic operating conditions, or in situ TEM imaging. The success of in situ TEM imaging is closely associated with advances in microfabrication techniques that enable manipulation of nanoscale objects around the objective lens of the TEM. This paper summarizes and highlights recent progress involving in situ TEM studies of energy storage materials, especially rechargeable batteries. The paper is organized to cover both the in situ TEM techniques and the scientific discoveries made possible by in situ TEM imaging.

  20. Moments of Spin Structure Functions: Sum Rules and Polarizabilities

    SciTech Connect

    Jian-Ping Chen

    2010-10-01

    Nucleon structure study is one of the most important research areas in modern physics and has challenged us for decades. Spin has played an essential role and often brought surprises and puzzles to the investigation of the nucleon structure and the strong interaction. New experimental data on nucleon spin structure at low to intermediate momentum transfers combined with existing high momentum transfer data offer a comprehensive picture in the strong region of the interaction and of the transition region from the strong to the asymptotic-free region. Insight for some aspects of the theory for the strong interaction, Quantum Chromodynamics (QCD), is gained by exploring lower moments of spin structure functions and their corresponding sum rules (i.e. the Bjorken, Burkhardt-Cottingham, Gerasimov-Drell-Hearn (GDH), and the generalized GDH). These moments are expressed in terms of an operator-product expansion using quark and gluon degrees of freedom at moderately large momentum transfers.

  1. In situ SEM Study of Lithium Intercalation in individual V2O5 Nanowires

    DOE PAGESBeta

    Strelcov, Evgheni; Cothren, Joshua E.; Leonard, Donovan N.; Borisevich, Albina Y.; Kolmakov, Andrei

    2015-01-08

    Progress in rational engineering of Li-ion batteries requires better understanding of the electrochemical processes and accompanying transformations in the electrode materials on multiple length scales. In spite of recent progress in utilizing transmission electron microscopy (TEM) to analyze these materials, in situ scanning electron microscopy (SEM) was mostly overlooked as a powerful tool that allows probing these phenomena on the nano and mesoscale. In this paper, we report on in situ SEM study of lithiation in a V2O5-based single-nanobelt battery with ionic liquid electrolyte. Coupled with cyclic voltammetry measurements, in situ SEM revealed the peculiarities of subsurface intercalation, formation ofmore » solid-electrolyte interface (SEI) and electromigration of liquid. We observed that single-crystalline vanadia nanobelts do not undergo large-scale amorphization or fracture during electrochemical cycling, but rather transform topochemically with only a slight shape distortion. Lastly, the SEI layer seems to have significant influence on the lithium ion diffusion and overall capacity of the single-nanobelt battery.« less

  2. An in situ approach to study trace element partitioning in the laser heated diamond anvil cell

    SciTech Connect

    Petitgirard, S.; Mezouar, M.; Borchert, M.; Appel, K.; Liermann, H.-P.; Andrault, D.

    2012-01-15

    Data on partitioning behavior of elements between different phases at in situ conditions are crucial for the understanding of element mobility especially for geochemical studies. Here, we present results of in situ partitioning of trace elements (Zr, Pd, and Ru) between silicate and iron melts, up to 50 GPa and 4200 K, using a modified laser heated diamond anvil cell (DAC). This new experimental set up allows simultaneous collection of x-ray fluorescence (XRF) and x-ray diffraction (XRD) data as a function of time using the high pressure beamline ID27 (ESRF, France). The technique enables the simultaneous detection of sample melting based to the appearance of diffuse scattering in the XRD pattern, characteristic of the structure factor of liquids, and measurements of elemental partitioning of the sample using XRF, before, during and after laser heating in the DAC. We were able to detect elements concentrations as low as a few ppm level (2-5 ppm) on standard solutions. In situ measurements are complimented by mapping of the chemical partitions of the trace elements after laser heating on the quenched samples to constrain the partitioning data. Our first results indicate a strong partitioning of Pd and Ru into the metallic phase, while Zr remains clearly incompatible with iron. This novel approach extends the pressure and temperature range of partitioning experiments derived from quenched samples from the large volume presses and could bring new insight to the early history of Earth.

  3. An in situ approach to study trace element partitioning in the laser heated diamond anvil cell.

    PubMed

    Petitgirard, S; Borchert, M; Andrault, D; Appel, K; Mezouar, M; Liermann, H-P

    2012-01-01

    Data on partitioning behavior of elements between different phases at in situ conditions are crucial for the understanding of element mobility especially for geochemical studies. Here, we present results of in situ partitioning of trace elements (Zr, Pd, and Ru) between silicate and iron melts, up to 50 GPa and 4200 K, using a modified laser heated diamond anvil cell (DAC). This new experimental set up allows simultaneous collection of x-ray fluorescence (XRF) and x-ray diffraction (XRD) data as a function of time using the high pressure beamline ID27 (ESRF, France). The technique enables the simultaneous detection of sample melting based to the appearance of diffuse scattering in the XRD pattern, characteristic of the structure factor of liquids, and measurements of elemental partitioning of the sample using XRF, before, during and after laser heating in the DAC. We were able to detect elements concentrations as low as a few ppm level (2-5 ppm) on standard solutions. In situ measurements are complimented by mapping of the chemical partitions of the trace elements after laser heating on the quenched samples to constrain the partitioning data. Our first results indicate a strong partitioning of Pd and Ru into the metallic phase, while Zr remains clearly incompatible with iron. This novel approach extends the pressure and temperature range of partitioning experiments derived from quenched samples from the large volume presses and could bring new insight to the early history of Earth. PMID:22299967

  4. In Situ Synchrotron X-Ray Techniques for the Study of Lithium Battery Materials

    SciTech Connect

    McBreen, J.; Mukerjee, S.; Yang, X. Q.; Sun, X., Ein-Eli, Y.

    1998-11-01

    The combination of in situ X-ray diffraction (XRD) and x-ray absorption spectroscopy (XAS) is a very powerful technique in the study of lithium battery cathode materials. XRD identifies the phase changes that occur during cycling and XAS gives information on the redox charge compensation processes that occur on the transition metal oxides. Because of its element specific nature XAS can identify the occurrence of redox processes on the various cations in doped oxide cathode materials. Since XAS probes short range order and is particularly useful in the study of amorphous tin based composite oxide anode materials.

  5. In situ vitrification and the effects of soil additives; A mixture experiment case study

    SciTech Connect

    Piepel, G.F.; Shade, J.W. )

    1992-01-01

    This paper presents a case study involving in situ vitrification (ISV), a process for immobilizing chemical or nuclear wastes in soil by melting-dissolving the contaminated soil into a glass block. One goal of the study was to investigate how viscosity and electrical conductivity were affected by mixing CaO and Na{sub 2}O with soil. A three-component constrained-region mixture experiment design was generated and the viscosity and electrical conductivity data collected. Several second-order mixture models were considered, and the Box-Cox transformation technique was applied to select property transformations. The fitted models were used to produce contour and component effects plots.

  6. In-situ x-ray absorption study of copper films in ground watersolutions

    SciTech Connect

    Kvashnina, K.O.; Butorin, S.M.; Modin, A.; Soroka, I.; Marcellini, M.; Nordgren, J.; Guo, J.-H.; Werme, L.

    2007-10-29

    This study illustrates how the damage from copper corrosion can be reduced by modifying the chemistry of the copper surface environment. The surface modification of oxidized copper films induced by chemical reaction with Cl{sup -} and HCO{sub 3}{sup -} in aqueous solutions was monitored by in situ X-ray absorption spectroscopy. The results show that corrosion of copper can be significantly reduced by adding even a small amount of sodium bicarbonate. The studied copper films corroded quickly in chloride solutions, whereas the same solution containing 1.1 mM HCO{sub 3}{sup -} prevented or slowed down the corrosion processes.

  7. In situ X-ray absorption study of copper films in ground water solutions

    NASA Astrophysics Data System (ADS)

    Kvashnina, K. O.; Butorin, S. M.; Modin, A.; Soroka, I.; Marcellini, M.; Nordgren, J.; Guo, J.-H.; Werme, L.

    2007-10-01

    This study illustrates how the damage from copper corrosion can be reduced by modifying the chemistry of the copper surface environment. The surface modification of oxidized copper films induced by chemical reaction with Cl - and HCO3- in aqueous solutions was monitored by in situ X-ray absorption spectroscopy. The results show that corrosion of copper can be significantly reduced by adding even a small amount of sodium bicarbonate. The studied copper films corroded quickly in chloride solutions, whereas the same solution containing 1.1 mM HCO3- prevented or slowed down the corrosion processes.

  8. A study of Mediterranean Eddies by in situ and remote sensing methods

    NASA Astrophysics Data System (ADS)

    Ienna, Federico Salvatore

    Subsurface coherent vortices in the North Atlantic, whose saline water originates from the Mediterranean Sea and which are known as Mediterranean Eddies ("meddies"), have been of particular interest to physical oceanographers since their discovery, especially for their salt and heat transport properties into the North Atlantic Ocean. Many studies in the past have been successful in observing and studying the typical properties of meddies by probing them with in-situ techniques. The use of remote sensing techniques would offer a much cheaper and easier alternative for studying these phenomena, but only a few past studies have been able to study meddies by remote sensing, and a reliable method for observing them remotely remains elusive. This research presents a new way of locating and tracking meddies in the North Atlantic Ocean using satellite altimeter data. The method presented in this research makes use of Ensemble Empirical Mode Decomposition (EEMD) as a mean to isolate the surface expressions of meddies on the ocean surface and separate them from any other surface constituents, allowing robust meddies to be consistently tracked by satellite. One such meddy is successfully tracked over a 6 month time period (2 November 2005 - 17 May 2006). Results of the satellite tracking method are verified using Expendable Bathythermographs (XBT). Furthermore, three other meddies are also studied by in-situ observations using Argo float data, and an analysis of the buoyancy frequency properties of meddies is made.

  9. Extracting Neutron Structure Functions in the Resonance Region

    SciTech Connect

    Yonatan Kahn

    2009-07-01

    A new iterative method is presented for extracting neutron structure functions from inclusive structure functions of nuclei, focusing specifically on the resonance region. Unlike earlier approaches, this method is applicable to both spin-averaged and spin-dependent structure functions. We show that in numerical tests, this method is able to reproduce known input functions of nearly arbitrary shape after only 5–10 iterations. We illustrate the method on extractions of F2n and g1,2n from data, and discuss the treatment of systematic errors from this extraction procedure.

  10. Electro-deposition of Cu studied with in situ electrochemical scanning transmission x-ray microscopy

    NASA Astrophysics Data System (ADS)

    Hitchcock, A. P.; Qin, Z.; Rosendahl, S. M.; Lee, V.; Reynolds, M.; Hosseinkhannazer, H.

    2016-01-01

    Soft X-ray scanning transmission X-ray microscopy (STXM) was used to investigate Cu deposition onto, and stripping from a Au surface. Cu 2p spectromicroscopy was used to analyze initial and final states (ex situ processing) and follow the processes in situ. The in situ experiments were carried out using a static electrochemical cell with an electrolyte layer thickness of ˜1 μm. A new apparatus for in situ electrochemical STXM is described.

  11. In situ study of atomic layer deposition Al2O3 on GaP (100)

    NASA Astrophysics Data System (ADS)

    Dong, H.; Brennan, B.; Qin, X.; Zhernokletov, D. M.; Hinkle, C. L.; Kim, J.; Wallace, R. M.

    2013-09-01

    The interfacial chemistry of atomic layer deposition (ALD) of Al2O3 on chemically treated GaP (100) has been studied using in situ X-ray photoelectron spectroscopy. A "self-cleaning" effect for Ga-oxide upon exposure to trimethylaluminum is seen to be efficient on the native oxide and chemically treated surfaces. The phosphorus oxide chemical states are seen to change during the ALD process, but the total concentration of P-oxides is seen to remain constant throughout the ALD process.

  12. XAFS characterization of industrial catalysts: in situ study of phase transformation of nickel sulfide

    NASA Astrophysics Data System (ADS)

    Wang, J.; Jia, Z.; Wang, Q.; Zhao, S.; Xu, Z.; Yang, W.; Frenkel, A. I.

    2016-05-01

    The online sulfiding process for nickel-contained catalyst often ends up with a nickel sulfide mixture in refinery plant. To elucidate the local environment of nickel and its corresponding sulfur species, a model catalyst (nickel sulfide) and model thermal process were employed to explore the possibilities for characterization of real catalysts in industrial conditions. The present investigation shows effectiveness of in situ XANES and EXAFS measurements for studying the phase stability and phase composition in these systems, which could be used to simulate real sulfiding process in industrial reactions, such as hydrodesulfurizations of oil.

  13. Application of in-situ bioassays with macrophytes in aquatic mesocosm studies.

    PubMed

    Coors, Anja; Kuckelkorn, Jochen; Hammers-Wirtz, Monika; Strauss, Tido

    2006-10-01

    Aquatic mesocosm studies assess ecotoxicological effects of chemicals by using small artificial ponds as models of lentic ecosystems. In this study, methods of controlled insertion of macrophytes within an outdoor mesocosm study were explored. Although analytically confirmed concentrations of the model herbicide terbuthylazine were high enough to expect direct effects on phytoplankton, functional parameters and dominant taxa abundance indicated only minor and transient effects. In-situ assays with Lemna minor, Myriophyllum spicatum, Potamogeton lucens and Chara globularis revealed adverse effects at concentrations in accordance with literature data. Complex interactions such as nutrient limitation and competition were possible reasons for the observed growth promotion at the lower concentration of about 5 microg/l terbuthylazine. The approach of macrophyte in-situ bioassays within a mesocosm study proved to be applicable. Presumed advantages are simultaneous acquisition of toxicity data for several species of aquatic plants under more realistic conditions compared to laboratory tests and inclusion of macrophytes as important structural and functional components in mesocosms while limiting their domination of the model ecosystem. PMID:16960660

  14. In situ and laboratory studies of bacterial survival using a microporous membrane sandwich.

    PubMed Central

    Granai, C; Sjogren, R E

    1981-01-01

    A new device and procedure for the study of bacterial survival in an aquatic environment are described. The device uses two appressed presterilized microporous membranes to expose a bacterial cell suspension to the environment at a cell concentration that closely resembles those levels found in natural aquatic ecosystems. The device has been used under laboratory controlled conditions and in situ to study and compare bacterial survival times. In laboratory studies, Escherichia coli and Streptococcus faecalis survived the longest at 12 degrees C, pH 5, and in the presence of iron or calcium ions and cysteine. Cells in mid-stationary growth phase survived longer than those in mid- or late-logarithmic phase, whereas those maintained for a year or more as stock cultures survived for shorter period of time than did recent environmental isolates. In situ studies indicate that 5% of the starting number of E. coli and S. faecalis cells may survive longer than 96 h at 16 degrees C in potable lake water, whereas survival times in polluted lake water were approximately 12 h. PMID:6784669

  15. In situ hybridization for the study of gene expression in neuro-otologic research.

    PubMed

    Wackym, P A; Popper, P; Ward, P H; Micevych, P E

    1990-10-01

    In situ hybridization histochemistry technology was developed for future application to neuro-otologic research. This method allowed the detection of cellular mRNA in tissue sections from the temporal bone or brainstem after cRNA/mRNA hybridization. To produce specific cRNA, single-stranded 35S-labeled cRNA (complimentary to target mRNA) is transcribed from commercially available plasmid vectors. These vectors contain promotor sequences for specific synthesis of RNA, and polylinker regions that will accept cloned DNA inserts for virtually any target nucleic acid sequence of interest. The protocol used in this research was optimized for studies that included concomitant immunohistochemical evaluation. The combination of in situ hybridization and immunohistochemistry provides the only method to correlate molecular information (gene expression) with biochemical or molecular markers, such as peptides or proteins (mRNA translation products) on individual cells in the temporal bone or brainstem. Using these techniques, we examined the distribution of the neuropeptide calcitonin gene-related peptide in rat temporal bone and brainstem sections using calcitonin gene-related peptide (CGRP) antisera and CGRP cRNA probes. We used in situ hybridization histochemistry with a cRNA probe complementary to the 3'-end noncoding sequence of the alpha CGRP mRNA and immunohistochemistry with a polyclonal antibody to the (TYR)CGRP23-37 to study the distribution of CGRP mRNA and CGRP-like immunoreactivity in the central and peripheral facial nerve. Numerous motoneuron cell bodies in the facial nucleus and accessory seventh nucleus and cell bodies in the gustatory geniculate ganglion were found to contain CGRP mRNA and the CGRP peptide.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:1701043

  16. Clinical in situ study investigating abrasive effects of two commercially available toothpastes.

    PubMed

    Giles, A; Claydon, N C A; Addy, M; Hughes, N; Sufi, F; West, N X

    2009-07-01

    The aim of this study was to determine if the abrasive effect on dentine of two commercially available toothpastes, known to vary in their in vitro abrasive levels, can be differentiated in an in situ model after 10 days, assessed by contact profilometry. This was a single centre, single blind, randomized, split mouth, two treatment, in situ study, in 34 healthy subjects, evaluating the abrasive effects of two marketed desensitizing toothpastes, (Colgate Sensitive Multi Protection toothpaste - C; Sensodyne Total Protection - S). Subjects wore bi-lateral, lower buccal appliances, each fitted with four dentine sections which were power brushed three times a day with the treatment regimen. Each subject received two toothpaste treatments for 10 days during the treatment period. Samples were measured at baseline and day 10 by contact and non-contact profilometry and day 5 by contact profilometry. Thirty-four subjects were included in the efficacy analysis. Results from contact profilometry showed statistically significant (P < 0.0001) dentine loss compared to baseline at day 5 and 10 for both pastes. At each time point, C showed statistically significantly greater dentine loss than S, P < 0.0001. After 10 days treatment, the difference in dentine loss between the pastes was 1.4 microm. The non-contact profilometry data showed similar trends. After 10 days of treatment, C showed statistically significantly greater dentine loss than S, with treatment difference of 0.9 microm, P = 0.0057. The methodology used has successfully differentiated between the abrasivity of the two pastes in respect of dentine surface loss over time in an in situ environment. PMID:19531090

  17. Structure, function and regulation of pyruvate carboxylase.

    PubMed Central

    Jitrapakdee, S; Wallace, J C

    1999-01-01

    Pyruvate carboxylase (PC; EC 6.4.1.1), a member of the biotin-dependent enzyme family, catalyses the ATP-dependent carboxylation of pyruvate to oxaloacetate. PC has been found in a wide variety of prokaryotes and eukaryotes. In mammals, PC plays a crucial role in gluconeogenesis and lipogenesis, in the biosynthesis of neurotransmitter substances, and in glucose-induced insulin secretion by pancreatic islets. The reaction catalysed by PC and the physical properties of the enzyme have been studied extensively. Although no high-resolution three-dimensional structure has yet been determined by X-ray crystallography, structural studies of PC have been conducted by electron microscopy, by limited proteolysis, and by cloning and sequencing of genes and cDNA encoding the enzyme. Most well characterized forms of active PC consist of four identical subunits arranged in a tetrahedron-like structure. Each subunit contains three functional domains: the biotin carboxylation domain, the transcarboxylation domain and the biotin carboxyl carrier domain. Different physiological conditions, including diabetes, hyperthyroidism, genetic obesity and postnatal development, increase the level of PC expression through transcriptional and translational mechanisms, whereas insulin inhibits PC expression. Glucocorticoids, glucagon and catecholamines cause an increase in PC activity or in the rate of pyruvate carboxylation in the short term. Molecular defects of PC in humans have recently been associated with four point mutations within the structural region of the PC gene, namely Val145-->Ala, Arg451-->Cys, Ala610-->Thr and Met743-->Thr. PMID:10229653

  18. Models of Protocellular Structure, Function and Evolution

    NASA Technical Reports Server (NTRS)

    New, Michael H.; Pohorille, Andrew; Szostak, Jack W.; Keefe, Tony; Lanyi, Janos K.; DeVincenzi, Donald L. (Technical Monitor)

    2001-01-01

    In the absence of any record of protocells, the most direct way to test our understanding, of the origin of cellular life is to construct laboratory models that capture important features of protocellular systems. Such efforts are currently underway in a collaborative project between NASA-Ames, Harvard Medical School and University of California. They are accompanied by computational studies aimed at explaining self-organization of simple molecules into ordered structures. The centerpiece of this project is a method for the in vitro evolution of protein enzymes toward arbitrary catalytic targets. A similar approach has already been developed for nucleic acids in which a small number of functional molecules are selected from a large, random population of candidates. The selected molecules are next vastly multiplied using the polymerase chain reaction.

  19. Oxidation Induced Doping of Nanoparticles Revealed by in Situ X-ray Absorption Studies.

    PubMed

    Kwon, Soon Gu; Chattopadhyay, Soma; Koo, Bonil; Dos Santos Claro, Paula Cecilia; Shibata, Tomohiro; Requejo, Félix G; Giovanetti, Lisandro J; Liu, Yuzi; Johnson, Christopher; Prakapenka, Vitali; Lee, Byeongdu; Shevchenko, Elena V

    2016-06-01

    Doping is a well-known approach to modulate the electronic and optical properties of nanoparticles (NPs). However, doping at nanoscale is still very challenging, and the reasons for that are not well understood. We studied the formation and doping process of iron and iron oxide NPs in real time by in situ synchrotron X-ray absorption spectroscopy. Our study revealed that the mass flow of the iron triggered by oxidation is responsible for the internalization of the dopant (molybdenum) adsorbed at the surface of the host iron NPs. The oxidation induced doping allows controlling the doping levels by varying the amount of dopant precursor. Our in situ studies also revealed that the dopant precursor substantially changes the reaction kinetics of formation of iron and iron oxide NPs. Thus, in the presence of dopant precursor we observed significantly faster decomposition rate of iron precursors and substantially higher stability of iron NPs against oxidation. The same doping mechanism and higher stability of host metal NPs against oxidation was observed for cobalt-based systems. Since the internalization of the adsorbed dopant at the surface of the host NPs is driven by the mass transport of the host, this mechanism can be potentially applied to introduce dopants into different oxidized forms of metal and metal alloy NPs providing the extra degree of compositional control in material design. PMID:27152970

  20. The g2 Structure Function: An Experimental Overview

    SciTech Connect

    Slifer, Karl

    2009-08-01

    We will discuss recent results for the spin structure functions, with an emphasis on g2 . High precision g2 data allows for tests of the Burkhardt-Cottingham sum rule, and is needed to consistently evaluate higher twist effects.

  1. Neutron structure function and A=3 mirror nuclei

    SciTech Connect

    Afnan, I.R.; Bissey, F.; Gomez, J.; Katramatou, A.T.; Melnitchouk, W.; Petratos, G.G.; Thomas, A.W.

    2000-06-01

    The authors demonstrate that the free neutron structure function can be extracted in deep-inelastic scattering from A=3 mirror nuclei, with nuclear effects canceling to within 2% for x {approx_lt} 0.85.

  2. Pentraxins: structure, function, and role in inflammation.

    PubMed

    Du Clos, Terry W

    2013-01-01

    The pentraxins are an ancient family of proteins with a unique architecture found as far back in evolution as the Horseshoe crab. In humans the two members of this family are C-reactive protein and serum amyloid P. Pentraxins are defined by their sequence homology, their pentameric structure and their calcium-dependent binding to their ligands. Pentraxins function as soluble pattern recognition molecules and one of the earliest and most important roles for these proteins is host defense primarily against pathogenic bacteria. They function as opsonins for pathogens through activation of the complement pathway and through binding to Fc gamma receptors. Pentraxins also recognize membrane phospholipids and nuclear components exposed on or released by damaged cells. CRP has a specific interaction with small nuclear ribonucleoproteins whereas SAP is a major recognition molecule for DNA, two nuclear autoantigens. Studies in autoimmune and inflammatory disease models suggest that pentraxins interact with macrophage Fc receptors to regulate the inflammatory response. Because CRP is a strong acute phase reactant it is widely used as a marker of inflammation and infection. PMID:24167754

  3. Structure-function relations in flavodoxins.

    PubMed

    Simondsen, R P; Tollin, G

    1980-12-10

    Flavodoxins are low molecular weight, FMN containing, proteins which function as electron transfer agents in a variety of microbial metabolic processes, including nitrogen fixation. Utilizing structural information obtained from x-ray crystal analysis, it has been possible to derive some new and important insights into the relationships which exist between flavin properties and protein environment by comparing the spectroscopic, thermodynamic and kinetic behavior of the flavodoxins with that of free flavin. Thus, for example, a qualitative understanding of the contribution of the protein to flavin redox potentials, semiquinone reactivity and mechanism of electron transfer is beginning to emerge. The highly negative redox potential required for the biochemical activity of the flavodoxins is accomplished by stabilizing the semiquinone via a hydrogen bond to the N-5 position of the flavin and destabilizing the fully-reduced form by constraining it to assume an unfavorable planar conformation. The reactivity of the semiquinone form is lowered by the aforementioned hydrogen bond, as well as by an interaction with a tryptophan residue in the binding site. Electron transfer is accomplished through the exposed dimethylbenzene ring of the bound coenzyme. Although it is not possible at present to determine the extent to which this understanding can be generalized to other flavoproteins, it is clear that a study of the flavodoxins will provide us with at least some of the principles which biological systems have used to modify flavin properties to fulfill a biochemical need. PMID:6782445

  4. Small catalytic RNA: Structure, function and application

    SciTech Connect

    Monforte, J.A.

    1991-04-01

    We have utilized a combination of photochemical cross-linking techniques and site-directed mutagenesis to obtain secondary and tertiary structure information for the self-cleaving, self-ligating subsequence of RNA from the negative strand of Satellite Tobacco Ringspot Virus. We have found that the helical regions fold about a hinge to promoting four different possible tertiary interactions, creating a molecular of similar shape to a paperclip. A model suggesting that the paperclip'' and hammerhead'' RNAs share a similar three dimensional structure is proposed. We have used a self-cleaving RNA molecule related to a subsequence of plant viroids, a hammerhead,'' to study the length-dependent folding of RNA produced during transcription by RNA polymerase. We have used this method to determine the length of RNA sequestered within elongating E. coli and T7 RNA polymerase complexes. The data show that for E. coli RNA polymerase 12{plus minus}1 nucleotides are sequestered within the ternary complex, which is consistent with the presence of an RNA-DNA hybrid within the transcription bubble, as proposed by others. The result for T7 RNA polymerase differs from E. coli RNA polymerase, with only 10{plus minus}1 nucleotides sequestered within the ternary complex, setting a new upper limit for the minimum RNA-DNA required for a stable elongating complex. Comparisons between E. coli and T7 RNA polymerase are made. The relevance of the results to models or transcription termination, abortive initiation, and initiation to elongation mode transitions are discussed.

  5. Islet Amyloid Polypeptide: Structure, Function, and Pathophysiology.

    PubMed

    Akter, Rehana; Cao, Ping; Noor, Harris; Ridgway, Zachary; Tu, Ling-Hsien; Wang, Hui; Wong, Amy G; Zhang, Xiaoxue; Abedini, Andisheh; Schmidt, Ann Marie; Raleigh, Daniel P

    2016-01-01

    The hormone islet amyloid polypeptide (IAPP, or amylin) plays a role in glucose homeostasis but aggregates to form islet amyloid in type-2 diabetes. Islet amyloid formation contributes to β-cell dysfunction and death in the disease and to the failure of islet transplants. Recent work suggests a role for IAPP aggregation in cardiovascular complications of type-2 diabetes and hints at a possible role in type-1 diabetes. The mechanisms of IAPP amyloid formation in vivo or in vitro are not understood and the mechanisms of IAPP induced β-cell death are not fully defined. Activation of the inflammasome, defects in autophagy, ER stress, generation of reactive oxygen species, membrane disruption, and receptor mediated mechanisms have all been proposed to play a role. Open questions in the field include the relative importance of the various mechanisms of β-cell death, the relevance of reductionist biophysical studies to the situation in vivo, the molecular mechanism of amyloid formation in vitro and in vivo, the factors which trigger amyloid formation in type-2 diabetes, the potential role of IAPP in type-1 diabetes, the development of clinically relevant inhibitors of islet amyloidosis toxicity, and the design of soluble, bioactive variants of IAPP for use as adjuncts to insulin therapy. PMID:26649319

  6. Islet Amyloid Polypeptide: Structure, Function, and Pathophysiology

    PubMed Central

    Akter, Rehana; Cao, Ping; Noor, Harris; Ridgway, Zachary; Tu, Ling-Hsien; Wang, Hui; Wong, Amy G.; Zhang, Xiaoxue; Abedini, Andisheh; Schmidt, Ann Marie; Raleigh, Daniel P.

    2016-01-01

    The hormone islet amyloid polypeptide (IAPP, or amylin) plays a role in glucose homeostasis but aggregates to form islet amyloid in type-2 diabetes. Islet amyloid formation contributes to β-cell dysfunction and death in the disease and to the failure of islet transplants. Recent work suggests a role for IAPP aggregation in cardiovascular complications of type-2 diabetes and hints at a possible role in type-1 diabetes. The mechanisms of IAPP amyloid formation in vivo or in vitro are not understood and the mechanisms of IAPP induced β-cell death are not fully defined. Activation of the inflammasome, defects in autophagy, ER stress, generation of reactive oxygen species, membrane disruption, and receptor mediated mechanisms have all been proposed to play a role. Open questions in the field include the relative importance of the various mechanisms of β-cell death, the relevance of reductionist biophysical studies to the situation in vivo, the molecular mechanism of amyloid formation in vitro and in vivo, the factors which trigger amyloid formation in type-2 diabetes, the potential role of IAPP in type-1 diabetes, the development of clinically relevant inhibitors of islet amyloidosis toxicity, and the design of soluble, bioactive variants of IAPP for use as adjuncts to insulin therapy. PMID:26649319

  7. Models of Protocellular Structure, Function and Evolution

    NASA Technical Reports Server (NTRS)

    New, Michael H.; Pohorille, Andrew; Szostak, Jack W.; Keefe, Tony; Lanyi, Janos K.

    2001-01-01

    In the absence of any record of protocells, the most direct way to test our understanding of the origin of cellular life is to construct laboratory models that capture important features of protocellular systems. Such efforts are currently underway in a collaborative project between NASA-Ames, Harvard Medical School and University of California. They are accompanied by computational studies aimed at explaining self-organization of simple molecules into ordered structures. The centerpiece of this project is a method for the in vitro evolution of protein enzymes toward arbitrary catalytic targets. A similar approach has already been developed for nucleic acids in which a small number of functional molecules are selected from a large, random population of candidates. The selected molecules are next vastly multiplied using the polymerase chain reaction. A mutagenic approach, in which the sequences of selected molecules are randomly altered, can yield further improvements in performance or alterations of specificities. Unfortunately, the catalytic potential of nucleic acids is rather limited. Proteins are more catalytically capable but cannot be directly amplified. In the new technique, this problem is circumvented by covalently linking each protein of the initial, diverse, pool to the RNA sequence that codes for it. Then, selection is performed on the proteins, but the nucleic acids are replicated. Additional information is contained in the original extended abstract.

  8. The nonsinglet structure function evolution by Laplace method

    SciTech Connect

    Boroun, G. R. E-mail: boroun@razi.ac.ir; Zarrin, S.

    2015-12-15

    We derive a general scheme for the evolution of the nonsinglet structure function at the leadingorder (LO) and next-to-leading-order (NLO) by using the Laplace-transform technique. Results for the nonsinglet structure function are compared with MSTW2008, GRV, and CKMT parameterizations and also EMC experimental data in the LO and NLO analysis. The results are in good agreement with the experimental data and other parameterizations in the low- and large-x regions.

  9. Polarized and Unpolarized Structure Functions in the Valon Model

    NASA Astrophysics Data System (ADS)

    Arash, Firooz

    2006-02-01

    Hadrons are considered as the bound states of their structureful constituents, the Valons. The valon structure is calculated perturbatively in QCD; which is universal and independent of the hosting hadron. This structure is used to calculate Proton and pion structure functions. For the case of polarized structure function, the valon representation, not only gives all the available data on gp,n,d1, but also requires a sizable orbital angular momentum associated with the partonic structure of the valon.

  10. Small catalytic RNA: Structure, function and application

    SciTech Connect

    Monforte, J.A.

    1991-04-01

    We have utilized a combination of photochemical cross-linking techniques and site-directed mutagenesis to obtain secondary and tertiary structure information for the self-cleaving, self-ligating subsequence of RNA from the negative strand of Satellite Tobacco Ringspot Virus. We have found that the helical regions fold about a hinge to promoting four different possible tertiary interactions, creating a molecular of similar shape to a paperclip. A model suggesting that the ``paperclip`` and ``hammerhead`` RNAs share a similar three dimensional structure is proposed. We have used a self-cleaving RNA molecule related to a subsequence of plant viroids, a ``hammerhead,`` to study the length-dependent folding of RNA produced during transcription by RNA polymerase. We have used this method to determine the length of RNA sequestered within elongating E. coli and T7 RNA polymerase complexes. The data show that for E. coli RNA polymerase 12{plus_minus}1 nucleotides are sequestered within the ternary complex, which is consistent with the presence of an RNA-DNA hybrid within the transcription bubble, as proposed by others. The result for T7 RNA polymerase differs from E. coli RNA polymerase, with only 10{plus_minus}1 nucleotides sequestered within the ternary complex, setting a new upper limit for the minimum RNA-DNA required for a stable elongating complex. Comparisons between E. coli and T7 RNA polymerase are made. The relevance of the results to models or transcription termination, abortive initiation, and initiation to elongation mode transitions are discussed.

  11. In Situ X-ray Diffraction Studies of Cathode Materials in Lithium Batteries

    SciTech Connect

    Yang, X. Q.; Sun, X.; McBreen, J.; Mukerjee, S.; Gao, Yuan; Yakovleva, M. V.; Xing, X. K.; Daroux, M. L.

    1998-11-01

    There is an increasing interest in lithiated transition metal oxides because of their use as cathodes in lithium batteries. LiCoO{sub 2}, LiNiO{sub 2} and LiMn{sub 2}O{sub 4} are the three most widely used and studied materials, At present, although it is relative expensive and toxic, LiCoO{sub 2} is the material of choice in commercial lithium ion batteries because of its ease of manufacture, better thermal stability and cycle life. However, the potential use of lithium ion batteries with larger capacity for power tools and electric vehicles in the future will demand new cathode materials with higher energy density, lower cost and better thermal stability. LiNiO{sub 2} is isostructural with LiCoO{sub 2}. It offers lower cost and high energy density than LiCoO{sub 2}. However, it has much poorer thermal stability than LiCoO{sub 2}, in the charged (delithiated) state. Co, Al, and other elements have been used to partially replace Ni in LiNiO{sub 2} system in order to increase the thermal stability. LiMn{sub 2}O{sub 4} has the highest thermal stability and lowest cost and toxicity. However, the low energy density and poor cycle life at elevated temperature are the major obstacles for this material. In order to develop safer, cheaper, and better performance cathode materials, the in-depth understanding of the relationships between the thermal stability and structure, performance and structure are very important. The performance here includes energy density and cycle life of the cathode materials. X-ray diffraction (XRD) is one of the most powerful tools to study these relationships. The pioneer ex situ XRD work on cathode materials for lithium batteries was done by Ohzuku. His XRD studies on LiMn{sub 2}O{sub 4}, LiCoO{sub 2}, LiNiO{sub 2}, LiNi{sub 0.5}Co{sub 0.5}O{sub 2}, and LiAl{sub x}Ni{sub 1-x}O{sub 2} cathodes at different states of charge have provided important guidelines for the development of these new materials. However, the kinetic nature of the battery

  12. Studies of ferroelectric heterostructure thin films and interfaces via in situ analytical techniques.

    SciTech Connect

    Auciello, O.; Dhote, A.; Gao, Y.; Gruen, D. M.; Im, J.; Irene, E. A.; Krauss, A. R.; Mueller, A. H.; Ramesh, R.

    1999-08-30

    The science and technology of ferroelectric thin films has experienced an explosive development during the last ten years. Low-density non-volatile ferroelectric random access memories (NVFRAMs) are now incorporated in commercial products such as ''smart cards'', while high permittivity capacitors are incorporated in cellular phones. However, substantial work is still needed to develop materials integration strategies for high-density memories. We have demonstrated that the implementation of complementary in situ characterization techniques is critical to understand film growth and interface processes, which play critical roles in film microstructure and properties. We are using uniquely integrated time of flight ion scattering and recoil spectroscopy (TOF-ISARS) and spectroscopic ellipsometry (SE) techniques to perform in situ, real-time studies of film growth processes in the high background gas pressure required to growth ferroelectric thin films. TOF-ISARS provides information on surface processes, while SE permits the investigation of buried interfaces as they are being formed. Recent studies on SrBi{sub 2}Ta{sub 2}O{sub 9} (SBT) and Ba{sub x}Sr{sub 1{minus}x}TiO{sub 3} (BST) film growth and interface processes are discussed.

  13. In situ USAXS studies of nano-particle growth in a premixed flame.

    NASA Astrophysics Data System (ADS)

    Beaucage, Gregory; Kammler, Hendrik; Kohls, Douglas; Ilavsky, Jan; Agashe, Nikhil; Pratsinis, Sotiris

    2003-03-01

    Combustion of organo-metallic or halide vapors and aerosol liquid sprays can be controlled to produce enormous quantities of nano-structured powders. Such flame processes are common in the production of fumed silica, and pyrolytic titania on an industrial scale with primary particle sizes on the order of 10 nm. These nano-particles are typically connected through sintering bridges, ionic bonds or van der Waals forces into ramified, mass-fractal aggregates. The study of this promising technology for nano-particle production has been hindered by the kinetics of particle growth, typically on the order of milliseconds, at high temperature, 2000°C. Using synchrotron radiation and specialized scattering instrumentation capable of simultaneously measuring nano- to colloidal scales (1 nm to 1µm) we demonstrate the feasibility of in situ growth studies in these systems and were able to follow in situ the growth of silica nanoparticles, namely the evolution of primary and agglomerate particle diameter and mass fractal dimension df.

  14. In Situ X-ray Reflectivity Studies of Protein Adsorption onto Functionalized Surfaces

    NASA Astrophysics Data System (ADS)

    Richter, Andrew

    2007-03-01

    The adsorption of protein films onto solid surfaces, both artificial and naturally occurring, have been widely studied using a variety of techniques due to their importance in medicine, biomedical applications, and the general understanding of protein structure and function. What have yet to be performed are in situ, time-resolved, high-resolution structural studies of these systems. We have begun a project that uses the technique of in situ x-ray reflectivity to obtain highly resolved structural information with time resolution on the order of minutes. This talk will present our first findings of serum albumin and immunoglobulin G films on hydrophobic self-assembled monolayers. The protein films are readily observable, showing extensive denaturing after adsorption with a slow decay of density into the aqueous solution. Additionally, a thin low-density region that occurs between the hydrophobic film and the solution persists after protein deposition. Comparisons to films that are removed from solution, the influence of solution concentration, the effects of x-ray damage, and the time scales for protein film formation and evolution will also be discussed.

  15. In-situ Study of Nanostructure and Electrical Resistance of Nanocluster Films Irradiated with Ion Beams

    SciTech Connect

    Jiang, Weilin; Sundararajan, Jennifer A.; Varga, Tamas; Bowden, Mark E.; Qiang, You; McCloy, John S.; Henager, Charles H.; Montgomery, Robert O.

    2014-08-11

    An in-situ study is reported on the structural evolution in nanocluster films under He+ ion irradiation using an advanced helium ion microscope. The films consist of loosely interconnected nanoclusters of magnetite or iron-magnetite (Fe-Fe3O4) core-shells. The nanostructure is observed to undergo dramatic changes under ion-beam irradiation, featuring grain growth, phase transition, particle aggregation, and formation of nanowire-like network and nano-pores. Studies based on ion irradiation, thermal annealing and election irradiation have indicated that the major structural evolution is activated by elastic nuclear collisions, while both electronic and thermal processes can play a significant role once the evolution starts. The electrical resistance of the Fe-Fe3O4 films measured in situ exhibits a super-exponential decay with dose. The behavior suggests that the nanocluster films possess an intrinsic merit for development of an advanced online monitor for neutron radiation with both high detection sensitivity and long-term applicability, which can enhance safety measures in many nuclear operations.

  16. In situ treatment of arsenic contaminated groundwater by aquifer iron coating: Experimental study.

    PubMed

    Xie, Xianjun; Wang, Yanxin; Pi, Kunfu; Liu, Chongxuan; Li, Junxia; Liu, Yaqing; Wang, Zhiqiang; Duan, Mengyu

    2015-09-15

    In situ arsenic removal from groundwater by an aquifer iron coating method has great potential to be a cost effective and simple groundwater remediation technology, especially in rural and remote areas where groundwater is used as the main water source for drinking. The in situ arsenic removal technology was first optimized by simulating arsenic removal in various quartz sand columns under anoxic conditions. The effectiveness was then evaluated in an actual high-arsenic groundwater environment. The arsenic removal mechanism by the coated iron oxide/hydroxide was investigated under different conditions using scanning electron microscopy (SEM)/X-ray absorption spectroscopy, electron probe microanalysis, and Fourier transformation infrared spectroscopy. Aquifer iron coating method was developed via a 4-step alternating injection of oxidant, iron salt and oxygen-free water. A continuous injection of 5.0 mmol/L FeSO4 and 2.5 mmol/L NaClO for 96 h can form a uniform goethite coating on the surface of quartz sand without causing clogging. At a flow rate of 7.2 mL/min of the injection reagents, arsenic (as Na2HAsO4) and tracer fluorescein sodium to pass through the iron-coated quartz sand column were approximately at 126 and 7 column pore volumes, respectively. The retardation factor of arsenic was 23.0, and the adsorption capacity was 0.11 mol As per mol Fe. In situ arsenic removal from groundwater in an aquifer was achieved by simultaneous injections of As(V) and Fe(II) reagents. Arsenic fixation resulted from a process of adsorption/co-precipitation with fine goethite particles by way of bidentate binuclear complexes. Therefore, the study results indicate that the high arsenic removal efficiency of the in situ aquifer iron coating technology likely resulted from the expanded specific surface area of the small goethite particles, which enhanced arsenic sorption capability and/or from co-precipitation of arsenic on the surface of goethite particles. PMID:25956146

  17. Mutation and structure-function relationships of cytochrome c

    SciTech Connect

    Sherman, F.

    1991-05-01

    The yeast cytochrome c system has become a key vehicle for structure- function studies in vitro using modern molecular genetic techniques to clarify fundamental aspects of the molecular evolutionary design of iso-1-cytochrome c (cyt c). The spectral properties of cyt c allow estimation of the number of molecules in vivo, and growth in lactate medium allows estimation of cyt c activity. Because most of our studies involve single copy replacements of CYC1, the cyt c gene, specific activities of altered forms of cyt c in vivo can be related to properties determined in vitro. We have identified five classes of cyt c mutants, and suggest mechanisms to account for each class of mutant. Lysine 77 is evolutionarily conserved in most eukaryotes; effect either in vitro or in vivo. CYC7 encodes iso-2-cytochrome c, another form of cyt c. CYC7 contains a non-AUG transcriptional start site, and was used to study initiation of protein synthesis at non- AUG codons. 3 refs.

  18. Structure-function investigations of bacterial photosynthetic reaction centers.

    PubMed

    Leonova, M M; Fufina, T Yu; Vasilieva, L G; Shuvalov, V A

    2011-12-01

    During photosynthesis light energy is converted into energy of chemical bonds through a series of electron and proton transfer reactions. Over the first ultrafast steps of photosynthesis that take place in the reaction center (RC) the quantum efficiency of the light energy transduction is nearly 100%. Compared to the plant and cyanobacterial photosystems, bacterial RCs are well studied and have relatively simple structure. Therefore they represent a useful model system both for manipulating of the electron transfer parameters to study detailed mechanisms of its separate steps as well as to investigate the common principles of the photosynthetic RC structure, function, and evolution. This review is focused on the research papers devoted to chemical and genetic modifications of the RCs of purple bacteria in order to study principles and mechanisms of their functioning. Investigations of the last two decades show that the maximal rates of the electron transfer reactions in the RC depend on a number of parameters. Chemical structure of the cofactors, distances between them, their relative orientation, and interactions to each other are of great importance for this process. By means of genetic and spectral methods, it was demonstrated that RC protein is also an essential factor affecting the efficiency of the photochemical charge separation. Finally, some of conservative water molecules found in RC not only contribute to stability of the protein structure, but are directly involved in the functioning of the complex. PMID:22339599

  19. In situ nanoindentation study on plasticity and work hardening in aluminium with incoherent twin boundaries

    NASA Astrophysics Data System (ADS)

    Bufford, D.; Liu, Y.; Wang, J.; Wang, H.; Zhang, X.

    2014-09-01

    Nanotwinned metals have been the focus of intense research recently, as twin boundaries may greatly enhance mechanical strength, while maintaining good ductility, electrical conductivity and thermal stability. Most prior studies have focused on low stacking-fault energy nanotwinned metals with coherent twin boundaries. In contrast, the plasticity of twinned high stacking-fault energy metals, such as aluminium with incoherent twin boundaries, has not been investigated. Here we report high work hardening capacity and plasticity in highly twinned aluminium containing abundant Σ3{112} incoherent twin boundaries based on in situ nanoindentation studies in a transmission electron microscope and corresponding molecular dynamics simulations. The simulations also reveal drastic differences in deformation mechanisms between nanotwinned copper and twinned aluminium ascribed to stacking-fault energy controlled dislocation-incoherent twin boundary interactions. This study provides new insight into incoherent twin boundary-dominated plasticity in high stacking-fault energy twinned metals.

  20. In situ vitrification: Numerical studies of coupled heat transfer and viscous flow processes

    NASA Astrophysics Data System (ADS)

    Carey, Graham F.; MacKinnon, Robert J.; Murray, Paul E.

    1990-09-01

    This report describes the formulation, results and conclusions of a series of numerical studies performed to support the Idaho National Engineering Laboratory (INEL) In Situ Vitrification (ISV) treatability study. These studies were designed to explore some of the questions related to the dominant physical phenomena associated with the coupled electric field, heat transfer, and fluid flow processes. The work examines the case of a 3-D axisymmetric problem with a central electrode. Such issues as the form of an electric heating model, choice of boundary conditions, latent heat effects, and conductive and convective transport are considered. Some important conclusions and recommendations are made in relation to the convective effects, determination of property parameters, and the issue of a valid electrical heating model.

  1. In situ vitrification: Numerical studies of coupled heat transfer and viscous flow processes

    SciTech Connect

    Carey, G.F.; MacKinnon, R.J.; Murray, P.E.

    1990-09-01

    This report describes the formulation, results and conclusions of a series of numerical studies performed to support the Idaho National Engineering Laboratory (INEL) In Situ Vitrification (ISV) treatability study. These studies were designed to explore some of the questions related to the dominant physical phenomena associated with the coupled electric field, heat transfer, and fluid flow processes. The work examines the case of a 3-D axisymmetric problem with a central electrode. Such issues as the form of an electric heating model, choice of boundary conditions, latent heat effects, and conductive and convective transport are considered. Some important conclusions and recommendations are made in relation to the convective effects, determination of property parameters, and the issue of a valid electrical heating model. 4 refs., 100 figs., 1 tab.

  2. In situ ambient pressure X-ray photoelectron spectroscopy studies of lithium-oxygen redox reactions.

    PubMed

    Lu, Yi-Chun; Crumlin, Ethan J; Veith, Gabriel M; Harding, Jonathon R; Mutoro, Eva; Baggetto, Loïc; Dudney, Nancy J; Liu, Zhi; Shao-Horn, Yang

    2012-01-01

    The lack of fundamental understanding of the oxygen reduction and oxygen evolution in nonaqueous electrolytes significantly hinders the development of rechargeable lithium-air batteries. Here we employ a solid-state Li(4+x)Ti(5)O(12)/LiPON/Li(x)V(2)O(5) cell and examine in situ the chemistry of Li-O(2) reaction products on Li(x)V(2)O(5) as a function of applied voltage under ultra high vacuum (UHV) and at 500 mtorr of oxygen pressure using ambient pressure X-ray photoelectron spectroscopy (APXPS). Under UHV, lithium intercalated into Li(x)V(2)O(5) while molecular oxygen was reduced to form lithium peroxide on Li(x)V(2)O(5) in the presence of oxygen upon discharge. Interestingly, the oxidation of Li(2)O(2) began at much lower overpotentials (~240 mV) than the charge overpotentials of conventional Li-O(2) cells with aprotic electrolytes (~1000 mV). Our study provides the first evidence of reversible lithium peroxide formation and decomposition in situ on an oxide surface using a solid-state cell, and new insights into the reaction mechanism of Li-O(2) chemistry. PMID:23056907

  3. In Situ Ambient Pressure X-ray Photoelectron Spectroscopy Studies of Lithium-Oxygen Redox Reactions

    PubMed Central

    Lu, Yi-Chun; Crumlin, Ethan J.; Veith, Gabriel M.; Harding, Jonathon R.; Mutoro, Eva; Baggetto, Loïc; Dudney, Nancy J.; Liu, Zhi; Shao-Horn, Yang

    2012-01-01

    The lack of fundamental understanding of the oxygen reduction and oxygen evolution in nonaqueous electrolytes significantly hinders the development of rechargeable lithium-air batteries. Here we employ a solid-state Li4+xTi5O12/LiPON/LixV2O5 cell and examine in situ the chemistry of Li-O2 reaction products on LixV2O5 as a function of applied voltage under ultra high vacuum (UHV) and at 500 mtorr of oxygen pressure using ambient pressure X-ray photoelectron spectroscopy (APXPS). Under UHV, lithium intercalated into LixV2O5 while molecular oxygen was reduced to form lithium peroxide on LixV2O5 in the presence of oxygen upon discharge. Interestingly, the oxidation of Li2O2 began at much lower overpotentials (~240 mV) than the charge overpotentials of conventional Li-O2 cells with aprotic electrolytes (~1000 mV). Our study provides the first evidence of reversible lithium peroxide formation and decomposition in situ on an oxide surface using a solid-state cell, and new insights into the reaction mechanism of Li-O2 chemistry. PMID:23056907

  4. An experimental system for high temperature X-ray diffraction studies with in situ mechanical loading

    PubMed Central

    Oswald, Benjamin B.; Schuren, Jay C.; Pagan, Darren C.; Miller, Matthew P.

    2013-01-01

    An experimental system with in situ thermomechanical loading has been developed to enable high energy synchrotron x-ray diffraction studies of crystalline materials. The system applies and maintains loads of up to 2250 N in uniaxial tension or compression at a frequency of up to 100 Hz. The furnace heats the specimen uniformly up to a maximum temperature of 1200 °C in a variety of atmospheres (oxidizing, inert, reducing) that, combined with in situ mechanical loading, can be used to mimic processing and operating conditions of engineering components. The loaded specimen is reoriented with respect to the incident beam of x-rays using two rotational axes to increase the number of crystal orientations interrogated. The system was used at the Cornell High Energy Synchrotron Source to conduct experiments on single crystal silicon and polycrystalline Low Solvus High Refractory nickel-based superalloy. The data from these experiments provide new insights into how stresses evolve at the crystal scale during thermomechanical loading and complement the development of high-fidelity material models. PMID:23556825

  5. In Situ Infrared Ellipsometry for Protein Adsorption Studies on Ultrathin Smart Polymer Brushes in Aqueous Environment.

    PubMed

    Kroning, Annika; Furchner, Andreas; Aulich, Dennis; Bittrich, Eva; Rauch, Sebastian; Uhlmann, Petra; Eichhorn, Klaus-Jochen; Seeber, Michael; Luzinov, Igor; Kilbey, S Michael; Lokitz, Bradley S; Minko, Sergiy; Hinrichs, Karsten

    2015-06-17

    The protein-adsorbing and -repelling properties of various smart nanometer-thin polymer brushes containing poly(N-isopropylacrylamide) and poly(acrylic acid) with high potential for biosensing and biomedical applications are studied by in situ infrared-spectroscopic ellipsometry (IRSE). IRSE is a highly sensitive nondestructive technique that allows protein adsorption on polymer brushes to be investigated in an aqueous environment as external stimuli, such as temperature and pH, are varied. These changes are relevant to conditions for regulation of protein adsorption and desorption for biotechnology, biocatalysis, and bioanalytical applications. Here brushes are used as model surfaces for controlling protein adsorption of human serum albumin and human fibrinogen. The important finding of this work is that IRSE in the in situ experiments in protein solutions can distinguish between contributions of polymer brushes and proteins. The vibrational bands of the polymers provide insights into the hydration state of the brushes, whereas the protein-specific amide bands are related to changes of the protein secondary structure. PMID:25668395

  6. In Situ Ambient Pressure X-ray Photoelectron Spectroscopy Studies of Lithium-Oxygen Redox Reactions

    NASA Astrophysics Data System (ADS)

    Lu, Yi-Chun; Crumlin, Ethan J.; Veith, Gabriel M.; Harding, Jonathon R.; Mutoro, Eva; Baggetto, Loïc; Dudney, Nancy J.; Liu, Zhi; Shao-Horn, Yang

    2012-10-01

    The lack of fundamental understanding of the oxygen reduction and oxygen evolution in nonaqueous electrolytes significantly hinders the development of rechargeable lithium-air batteries. Here we employ a solid-state Li4+xTi5O12/LiPON/LixV2O5 cell and examine in situ the chemistry of Li-O2 reaction products on LixV2O5 as a function of applied voltage under ultra high vacuum (UHV) and at 500 mtorr of oxygen pressure using ambient pressure X-ray photoelectron spectroscopy (APXPS). Under UHV, lithium intercalated into LixV2O5 while molecular oxygen was reduced to form lithium peroxide on LixV2O5 in the presence of oxygen upon discharge. Interestingly, the oxidation of Li2O2 began at much lower overpotentials (~240 mV) than the charge overpotentials of conventional Li-O2 cells with aprotic electrolytes (~1000 mV). Our study provides the first evidence of reversible lithium peroxide formation and decomposition in situ on an oxide surface using a solid-state cell, and new insights into the reaction mechanism of Li-O2 chemistry.

  7. Fluorescence in situ detection of human cutaneous melanoma: study of diagnostic parameters of the method.

    PubMed

    Chwirot, B W; Chwirot, S; Sypniewska, N; Michniewicz, Z; Redzinski, J; Kurzawski, G; Ruka, W

    2001-12-01

    Multicenter study of the diagnostic parameters was conducted by three groups in Poland to determine if in situ fluorescence detection of human cutaneous melanoma based on digital imaging of spectrally resolved autofluorescence can be used as a tool for a preliminary selection of patients at increased risk of the disease. Fluorescence examinations were performed for 7228 pigmented lesions in 4079 subjects. Histopathologic examinations showed 56 cases of melanoma. A sensitivity of fluorescence detection of melanoma was 82.7% in agreement with 82.5% found in earlier work. Using as a reference only the results of histopathologic examinations obtained for 568 cases we found a specificity of 59.9% and a positive predictive value of 17.5% (melanomas versus all pigmented lesions) or 24% (melanomas versus common and dysplastic naevi). The specificity and positive predictive value found in this work are significantly lower than reported earlier but still comparable with those reported for typical screening programs. In conclusion, the fluorescence method of in situ detection of melanoma can be used in screening large populations of patients for a selection of patients who should be examined by specialists. PMID:11886507

  8. In Situ Single-Nanoparticle Spectroscopy Study of Bimetallic Nanostructure Formation.

    PubMed

    Smith, Jeremy G; Chakraborty, Indranath; Jain, Prashant K

    2016-08-16

    Bimetallic nanostructures (NSs), with utility in catalysis, are typically prepared using galvanic exchange (GE), but the final catalyst morphology is dictated by the dynamics of the process. In situ single nanoparticle (NP) optical scattering spectroscopy, coupled with ex situ electron microscopy, is used to capture the dynamic structural evolution of a bimetallic NS formed in a GE reaction between Ag and [PtCl6 ](2-) . We identify an early stage involving anisotropic oxidation of Ag to AgCl concomitant with reductive deposition of small Pt clusters on the NS surface. At later stages of GE, unreacted Ag inclusions phase segregate from the overcoated AgCl as a result of lattice strain between Ag and AgCl. The nature of the structural evolution elucidates why multi-domain Ag/AgCl/Pt NSs result from the GE process. The complex structural dynamics, determined from single-NP trajectories, would be masked in ensemble studies due to heterogeneity in the response of different NPs. PMID:27381891

  9. Prioritising in situ conservation of crop resources: a case study of African cowpea (Vigna unguiculata).

    PubMed

    Moray, C; Game, E T; Maxted, N

    2014-01-01

    Conserving crop wild relatives (CWR) is critical for maintaining food security. However, CWR-focused conservation plans are lacking, and are often based on the entire genus, even though only a few taxa are useful for crop improvement. We used taxonomic and geographic prioritisation to identify the best locations for in situ conservation of the most important (priority) CWR, using African cowpea (Vigna unguiculata (L.) Walp.) as a case study. Cowpea is an important crop for subsistence farmers in sub-Saharan Africa, yet its CWR are under-collected, under-conserved and under-utilised in breeding. We identified the most efficient sites to focus in situ cowpea CWR conservation and assessed whether priority CWR would be adequately represented in a genus-based conservation plan. We also investigated whether priority cowpea CWR are likely to be found in existing conservation areas and in areas important for mammal conservation. The genus-based method captured most priority CWR, and the distributions of many priority CWR overlapped with established conservation reserves and targets. These results suggest that priority cowpea CWR can be conserved by building on conservation initiatives established for other species. PMID:24936740

  10. Reversible Morphology Control in Block Copolymer Films via Solvent Vapor Processing: An In Situ GISAXS study

    PubMed Central

    Paik, Marvin Y.; Bosworth, Joan K.; Smilges, Detlef-M.; Schwartz, Evan L.; Andre, Xavier; Ober, Christopher K.

    2010-01-01

    The real time changes occurring within films of cylinder-forming poly(α-methylstyrene-block-4-hydroxystyrene) (PαMS-b-PHOST) were monitored as they were swollen in tetrahydrofuran (THF) and acetone solvent vapors. In situ information was obtained by combining grazing incidence small angle X-ray scattering (GISAXS) with film thickness monitoring of the solvent vapor swollen films. We show that for self assembly to occur, the polymer thin film must surpass a swollen thickness ratio of 212% of its original thickness when swollen in THF vapors and a ratio of 268% for acetone vapor annealing. As the polymer becomes plasticized by solvent vapor uptake, the polymer chains must become sufficiently mobile to self assemble, or reorganize, at room temperature. Using vapors of a solvent selective to one of the blocks, in our case PHOST-selective acetone, an order-order transition occured driven by the shift in volume fraction. The BCC spherical phase assumed in the highly swollen state can be quenched by rapid drying. Upon treatment with vapor of a non-selective solvent, THF, the film maintained the cylindrical morphology suggested by its dry-state volume fraction. In situ studies indicate that self-assembly occurs spontaneously upon attaining the threshold swelling ratios. PMID:21116459

  11. Prioritising in situ conservation of crop resources: A case study of African cowpea (Vigna unguiculata)

    PubMed Central

    Moray, C.; Game, E. T.; Maxted, N.

    2014-01-01

    Conserving crop wild relatives (CWR) is critical for maintaining food security. However, CWR-focused conservation plans are lacking, and are often based on the entire genus, even though only a few taxa are useful for crop improvement. We used taxonomic and geographic prioritisation to identify the best locations for in situ conservation of the most important (priority) CWR, using African cowpea (Vigna unguiculata (L.) Walp.) as a case study. Cowpea is an important crop for subsistence farmers in sub-Saharan Africa, yet its CWR are under-collected, under-conserved and under-utilised in breeding. We identified the most efficient sites to focus in situ cowpea CWR conservation and assessed whether priority CWR would be adequately represented in a genus-based conservation plan. We also investigated whether priority cowpea CWR are likely to be found in existing conservation areas and in areas important for mammal conservation. The genus-based method captured most priority CWR, and the distributions of many priority CWR overlapped with established conservation reserves and targets. These results suggest that priority cowpea CWR can be conserved by building on conservation initiatives established for other species. PMID:24936740

  12. Spatial Variances of Wind Fields and Their Relation to Second-Order Structure Functions and Spectra

    NASA Astrophysics Data System (ADS)

    King, G. P.; Vogelzang, J.; Stoffelen, A.; Portabella, M.

    2014-12-01

    Kinetic energy variance as a function of spatial scale for wind fields is commonly estimated either using second-order structure functions (in the spatial domain) or by spectral analysis (in the frequency domain). It will be demonstrated that neither spectra nor second-order structure functions offer a good representation of the variance as a function of scale. These difficulties can be circumvented by using a statistical quantity called spatial variance. It combines the advantages of spectral analysis and spatial statistics. In particular, when applied to observations, spatial variances have a clear interpretation and are tolerant for missing data. They can be related to second-order structure functions, both for discrete and continuous data. For data sets without missing points the relation is statistically exact. Spatial variances can also be Fourier transformed to yield a relation with spectra. The flexibility of spatial variances is used to study various sampling strategies, and to compare them with second-order structure functions and spectral variances. It is shown that the spectral sampling strategy is not seriously biased to calm conditions for scatterometer ocean surface vector winds, and that one-fifth of the second-order structure function value is a good proxy for the cumulative variance.

  13. Androgen Receptor Structure, Function and Biology: From Bench to Bedside

    PubMed Central

    Davey, Rachel A; Grossmann, Mathis

    2016-01-01

    The actions of androgens such as testosterone and dihydrotestosterone are mediated via the androgen receptor (AR), a ligand-dependent nuclear transcription factor and member of the steroid hormone nuclear receptor family. Given its widespread expression in many cells and tissues, the AR has a diverse range of biological actions including important roles in the development and maintenance of the reproductive, musculoskeletal, cardiovascular, immune, neural and haemopoietic systems. AR signalling may also be involved in the development of tumours in the prostate, bladder, liver, kidney and lung. Androgens can exert their actions via the AR in a DNA binding-dependent manner to regulate target gene transcription, or in a non-DNA binding-dependent manner to initiate rapid, cellular events such as the phosphorylation of 2nd messenger signalling cascades. More recently, ligand-independent actions of the AR have also been identified. Given the large volume of studies relating to androgens and the AR, this review is not intended as an extensive review of all studies investigating the AR, but rather as an overview of the structure, function, signalling pathways and biology of the AR as well as its important role in clinical medicine, with emphasis on recent developments in this field. PMID:27057074

  14. Studies of in-situ calcium-based sorbents in advanced pressurized coal conversion systems

    SciTech Connect

    Katta, S.; Shires, P.J.; O'Donnell, J.J.

    1992-01-01

    The overall objective of the project is to obtain experimental data on the reactions of calcium-based sorbents in gasification systems and to evaluate or develop kinetic models applicable to the commercial design of such systems. Both air-blown coal gasification systems and second generation fluid bed combustion systems (partial gasification) will be investigated, as well as subsequent stabilization of the solid wastes (calcium sulfide/ash) produced. More specifically, the objectives are to: Develop data on kinetics of in-situ desulfurization reactions; study the effect of calcium on the kinetics of carbon conversion rate; study kinetics of oxidation of CaS to CaSO[sup 4]; Develop and identify viable techniques to stabilize CaS; and, carry out further development work on most promising method and determine its commercial economics.

  15. Studies of in-situ calcium-based sorbents in advanced pressurized coal conversion systems

    SciTech Connect

    Katta, S.; Shires, P.J.; O`Donnell, J.J.

    1992-11-01

    The overall objective of the project is to obtain experimental data on the reactions of calcium-based sorbents in gasification systems and to evaluate or develop kinetic models applicable to the commercial design of such systems. Both air-blown coal gasification systems and second generation fluid bed combustion systems (partial gasification) will be investigated, as well as subsequent stabilization of the solid wastes (calcium sulfide/ash) produced. More specifically, the objectives are to: Develop data on kinetics of in-situ desulfurization reactions; study the effect of calcium on the kinetics of carbon conversion rate; study kinetics of oxidation of CaS to CaSO{sup 4}; Develop and identify viable techniques to stabilize CaS; and, carry out further development work on most promising method and determine its commercial economics.

  16. Acquired cystic disease-associated renal cell carcinoma: an immunohistochemical and fluorescence in situ hybridization study.

    PubMed

    Kuroda, Naoto; Yamashita, Motoki; Kakehi, Yoshiyuki; Hes, Ondrej; Michal, Michal; Lee, Gang-Hong

    2011-12-01

    Acquired cystic disease (ACD)-associated renal cell carcinoma (RCC) has been recently identified. However, there are only a few genetic studies to date. In this article, we performed an immunohistochemical and fluorescence in situ hybridization (FISH) study for six cases including one case with sarcomatoid change. As a result, we observed frequent immunohistochemical expression of AMACR. FISH of chromosome 3 showed trisomy for three cases, monosomy for two cases, and disomy for one case. Additionally, FISH of chromosome 16 showed trisomy for three cases, monosomy for two cases, and both trisomy and monosomy for one case. Furthermore, both the carcinomatous area and the sarcomatoid area of one ACD-associated RCC with sarcomatoid change revealed monosomy of chromosomes 3, 9, and 16 but showed disomy of chromosome 14. In conclusion, the numerical abnormalities of chromosomes 3 and 16, irrespective of gain or loss, may be characteristic of ACD-associated RCC. PMID:22179186

  17. Study of SGD along the French Mediterranean coastline using airborne TIR images and in situ analyses

    NASA Astrophysics Data System (ADS)

    van Beek, Pieter; Stieglitz, Thomas; Souhaut, Marc

    2015-04-01

    Although submarine groundwater discharge (SGD) has been investigated in many places of the world, very few studies were conducted along the French coastline of the Mediterranean Sea. Almost no information is available on the fluxes of water and chemical elements associated with these SGD and on their potential impact on the geochemical cycling and ecosystems of the coastal zones. In this work, we combined the use of airborne thermal infrared (TIR) images with in situ analyses of salinity, temperature, radon and radium isotopes to study SGD at various sites along the French Mediterranean coastline and in coastal lagoons. These analyses allowed us to detect SGD sites and to quantify SGD fluxes (that include both the fluxes of fresh groundwater and recirculated seawater). In particular, we will show how the Ra isotopes determined in the La Palme lagoon were used to estimate i) the residence time of waters in the lagoon and ii) SGD fluxes.

  18. Manipulating the Assembly of Spray-Deposited Nanocolloids: In Situ Study and Monolayer Film Preparation.

    PubMed

    Zhang, Peng; Santoro, Gonzalo; Yu, Shun; Vayalil, Sarathlal K; Bommel, Sebastian; Roth, Stephan V

    2016-05-01

    Fabrication of nanoparticle arrays on a substrate is one of the most concerned aspects for manipulating assembly of nanoparticles and preparing functional nanocomposites. Here, we studied in situ the assembly kinetics of polystyrene nanocolloids by using grazing incidence small-angle X-ray scattering. The structure formation of the nanoparticle film is monitored during air-brush spraying, which provides a rapid and scalable preparation. By optimizing the substrate temperature, the dispersion of the nanocolloids can be tailored to prepare monolayer film. The success of the monolayer preparations is attributed to the fast solvent evaporation which inhibits the aggregation of the nanocolloids. The present study may open a new avenue for the manufacture-friendly preparation of well-dispersed nanoparticle thin films. PMID:27070283

  19. Remediation case studies: Ex situ soil treatment technologies (bioremediation, solvent extraction, thermal desorption). Volume 7

    SciTech Connect

    1998-09-01

    The case studies in this volume describe ten applications of ex situ soil treatment technologies, including three applications of land treatment (bioremediation), one application of solvent extraction, and six applications of thermal desorption. Two of the land treatment applications were full-scale remediations of sites contaminated with polycyclic aromatic hydrocarbons (PAHs) and petroleum hydrocarbons, and one was a field demonstration at a site contaminated with pesticides. The solvent extraction application was a full-scale application to treat soil contaminated with PCBs. All six thermal desorption applications were full-scale, and involved treatment of soil contaminated with chlorinated solvents, petroleum hydrocarbons, PAHs, and pesticides. All case studies in this volume are for completed applications.

  20. The Impact of the Structure, Function, and Resources of the Campus Security Office on Campus Safety

    ERIC Educational Resources Information Center

    Bennett, Patricia Anne

    2012-01-01

    The topic of this dissertation is college and university safety. This national quantitative study utilized resource dependency theory to examine relationships between the incidence of reported campus crimes and the structure, function, and resources of campus security offices. This study uncovered a difference in reported total crime rates,…

  1. In-hospital resuscitation evaluated by in situ simulation: a prospective simulation study

    PubMed Central

    2011-01-01

    Background Interruption in chest compressions during cardiopulmonary resuscitation can be characterized as no flow ratio (NFR) and the importance of minimizing these pauses in chest compression has been highlighted recently. Further, documentation of resuscitation performance has been reported to be insufficient and there is a lack of identification of important issues where future efforts might be beneficial. By implementing in situ simulation we created a model to evaluate resuscitation performance. The aims of the study were to evaluate the feasibility of the applied method, and to examine differences in the resuscitation performance between the first responders and the cardiac arrest team. Methods A prospective observational study of 16 unannounced simulated cardiopulmonary arrest scenarios was conducted. The participants of the study involved all health care personel on duty who responded to a cardiac arrest. We measured NFR and time to detection of initial rhythm on defibrillator and performed a comparison between the first responders and the cardiac arrest team. Results Data from 13 out of 16 simulations was used to evaluate the ability of generating resuscitation performance data in simulated cardiac arrest. The defibrillator arrived after median 214 seconds (180-254) and detected initial rhythm after median 311 seconds (283-349). A significant difference in no flow ratio (NFR) was observed between the first responders, median NFR 38% (32-46), and the resuscitation teams, median NFR 25% (19-29), p < 0.001. The difference was significant even after adjusting for pulse and rhythm check and shock delivery. Conclusion The main finding of this study was a significant difference between the first responders and the cardiac arrest team with the latter performing more adequate cardiopulmonary resuscitation with regards to NFR. Future research should focus on the educational potential for in-situ simulation in terms of improving skills of hospital staff and patient

  2. Comparison between in situ and ex situ gamma measurements on land areas within a decommissioning nuclear site: a case study at Dounreay.

    PubMed

    Rostron, Peter D; Heathcote, John A; Ramsey, Michael H

    2014-09-01

    Measurements made in situ with gamma detectors and ex situ measurements of soil samples in a laboratory can have complementary roles in the assessment of radioactively contaminated land on decommissioning nuclear sites. Both in situ and ex situ methods were used to characterize (137)Cs contamination within an area at the Dounreay site in Scotland. The systematic difference (bias) between estimates of the mean activity concentration was found to be non-significant when in situ measurements were interpreted using a linear depth model, based on ex situ measurements made at two different depths. An established method of evaluating the random components of measurement uncertainty was used. The random component of analytical uncertainty in the in situ measurements, made in field conditions, was found to exceed that for the ex situ measurements, made in the controlled conditions of a laboratory. However, contamination by the target radionuclide was found to be heterogeneous over small spatial scales. This resulted in significantly higher levels of random sampling uncertainty in individual ex situ measurements. As in situ measurements are substantially less costly, a greater number of measurements can be made, which potentially reduces the uncertainty on the mean. Providing the depth profile of contaminants can be modelled with confidence, this can enable estimates of mean activity concentration over an averaging area to be made with lower overall uncertainties than are possible using ex situ methods. PMID:24938421

  3. Preliminary Results on the Experimental Investigation of the Structure Functions of Bound Nucleons

    SciTech Connect

    Bodek, Arie

    2015-09-01

    We present preliminary results on an experimental study of the nuclear modification of the longitudinal (σL) and transverse (σT) structure functions of nucleons bound in nuclear targets. The origin of these modifications (commonly referred as as the EMC effect) is not fully understood. Our measurements of R= σLT for nuclei (RA) and for deuterium (RD) indicate that nuclear modifications of the structure functions of bound nucleons are different for the longitudinal and transverse structure functions, and that contrary to expectation from several theoretical models, RA < RD.

  4. Neurolinguistics: Structure, Function, and Connectivity in the Bilingual Brain.

    PubMed

    Wong, Becky; Yin, Bin; O'Brien, Beth

    2016-01-01

    Advances in neuroimaging techniques and analytic methods have led to a proliferation of studies investigating the impact of bilingualism on the cognitive and brain systems in humans. Lately, these findings have attracted much interest and debate in the field, leading to a number of recent commentaries and reviews. Here, we contribute to the ongoing discussion by compiling and interpreting the plethora of findings that relate to the structural, functional, and connective changes in the brain that ensue from bilingualism. In doing so, we integrate theoretical models and empirical findings from linguistics, cognitive/developmental psychology, and neuroscience to examine the following issues: (1) whether the language neural network is different for first (dominant) versus second (nondominant) language processing; (2) the effects of bilinguals' executive functioning on the structure and function of the "universal" language neural network; (3) the differential effects of bilingualism on phonological, lexical-semantic, and syntactic aspects of language processing on the brain; and (4) the effects of age of acquisition and proficiency of the user's second language in the bilingual brain, and how these have implications for future research in neurolinguistics. PMID:26881224

  5. Ion Channel Voltage Sensors: Structure, Function, and Pathophysiology

    PubMed Central

    Catterall, William A.

    2010-01-01

    Voltage-gated ion channels generate electrical signals in species from bacteria to man. Their voltage-sensing modules are responsible for initiation of action potentials and graded membrane potential changes in response to synaptic input and other physiological stimuli. Extensive structure-function studies, structure determination, and molecular modeling are now converging on a sliding-helix mechanism for electromechanical coupling in which outward movement of gating charges in the S4 transmembrane segments catalyzed by sequential formation of ion pairs pulls the S4-S5 linker, bends the S6 segment, and opens the pore. Impairment of voltage-sensor function by mutations in Na+ channels contributes to several ion channelopathies, and gating pore current conducted by mutant voltage sensors in NaV1.4 channels is the primary pathophysiological mechanism in Hypokalemic Periodic Paralysis. The emerging structural model for voltage sensor function opens the way to development of a new generation of ionchannel drugs that act on voltage sensors rather than blocking the pore. PMID:20869590

  6. Ion channel voltage sensors: structure, function, and pathophysiology.

    PubMed

    Catterall, William A

    2010-09-23

    Voltage-gated ion channels generate electrical signals in species from bacteria to man. Their voltage-sensing modules are responsible for initiation of action potentials and graded membrane potential changes in response to synaptic input and other physiological stimuli. Extensive structure-function studies, structure determination, and molecular modeling are now converging on a sliding-helix mechanism for electromechanical coupling in which outward movement of gating charges in the S4 transmembrane segments catalyzed by sequential formation of ion pairs pulls the S4-S5 linker, bends the S6 segment, and opens the pore. Impairment of voltage-sensor function by mutations in Na+ channels contributes to several ion channelopathies, and gating pore current conducted by mutant voltage sensors in Na(V)1.4 channels is the primary pathophysiological mechanism in hypokalemic periodic paralysis. The emerging structural model for voltage sensor function opens the way to development of a new generation of ion-channel drugs that act on voltage sensors rather than blocking the pore. PMID:20869590

  7. Structure/Function/Dynamics of Photosystem II Plastoquinone Binding Sites

    PubMed Central

    Lambreva, Maya D.; Russo, Daniela; Polticelli, Fabio; Scognamiglio, Viviana; Antonacci, Amina; Zobnina, Veranika; Campi, Gaetano; Rea, Giuseppina

    2014-01-01

    Photosystem II (PSII) continuously attracts the attention of researchers aiming to unravel the riddle of its functioning and efficiency fundamental for all life on Earth. Besides, an increasing number of biotechnological applications have been envisaged exploiting and mimicking the unique properties of this macromolecular pigment-protein complex. The PSII organization and working principles have inspired the design of electrochemical water splitting schemes and charge separating triads in energy storage systems as well as biochips and sensors for environmental, agricultural and industrial screening of toxic compounds. An intriguing opportunity is the development of sensor devices, exploiting native or manipulated PSII complexes or ad hoc synthesized polypeptides mimicking the PSII reaction centre proteins as bio-sensing elements. This review offers a concise overview of the recent improvements in the understanding of structure and function of PSII donor side, with focus on the interactions of the plastoquinone cofactors with the surrounding environment and operational features. Furthermore, studies focused on photosynthetic proteins structure/function/dynamics and computational analyses aimed at rational design of high-quality bio-recognition elements in biosensor devices are discussed. PMID:24678671

  8. Neurolinguistics: Structure, Function, and Connectivity in the Bilingual Brain

    PubMed Central

    Wong, Becky; Yin, Bin; O'Brien, Beth

    2016-01-01

    Advances in neuroimaging techniques and analytic methods have led to a proliferation of studies investigating the impact of bilingualism on the cognitive and brain systems in humans. Lately, these findings have attracted much interest and debate in the field, leading to a number of recent commentaries and reviews. Here, we contribute to the ongoing discussion by compiling and interpreting the plethora of findings that relate to the structural, functional, and connective changes in the brain that ensue from bilingualism. In doing so, we integrate theoretical models and empirical findings from linguistics, cognitive/developmental psychology, and neuroscience to examine the following issues: (1) whether the language neural network is different for first (dominant) versus second (nondominant) language processing; (2) the effects of bilinguals' executive functioning on the structure and function of the “universal” language neural network; (3) the differential effects of bilingualism on phonological, lexical-semantic, and syntactic aspects of language processing on the brain; and (4) the effects of age of acquisition and proficiency of the user's second language in the bilingual brain, and how these have implications for future research in neurolinguistics. PMID:26881224

  9. Multiphoton microscopy: an efficient tool for in-situ study of cultural heritage artifacts

    NASA Astrophysics Data System (ADS)

    Latour, Gaël.; Echard, Jean-Philippe; Didier, Marie; Schanne-Klein, Marie-Claire

    2013-05-01

    We present multimodal nonlinear optical imaging of historical artifacts by combining Two-Photon Excited Fluorescence (2PEF) and Second Harmonic Generation (SHG) microscopies. Three-dimensional (3D) non-contact laser-scanning imaging with micrometer resolution is performed without any preparation of the objects under study. 2PEF signals are emitted by a wide range of fluorophores such as pigments and binder, which can be discriminated thanks to their different emission spectral bands by using suitable spectral filters in the detection channel. SHG signals are specific for dense non-centrosymmetric organizations such as the crystalline cellulose within the wood cell walls. We also show that plaster particles exhibit SHG signals. These particles are bassanite crystals with a non-centrosymmetric crystalline structure, while the other types of calcium sulphates exhibit a centrosymmetric crystalline structure with no SHG signal. In our study, we first characterize model single-layered samples: wood, gelatin-based films containing plaster or cochineal lake and sandarac film containing cochineal lake. We then study multilayered coating systems on wood and show that multimodal nonlinear microscopy successfully reveals the 3D distribution of all components within the stratified sample. We also show that the fine structure of the wood can be assessed, even through a thick multilayered varnish coating. Finally, in situ multimodal nonlinear imaging is demonstrated in a historical violin. SHG/2PEF imaging thus appears as an efficient non-destructive and contactless 3D imaging technique for in situ investigation of historical coatings and more generally for wood characterization and coating analysis at micrometer scale.

  10. In Situ Nanoindentation Studies on Detwinning and Work Hardening in Nanotwinned Monolithic Metals

    SciTech Connect

    Liu, Y.; Li, N.; Bufford, D.; Lee, J. H.; Wang, J.; Wang, H.; Zhang, X.

    2015-07-14

    Certain nanotwinned (nt) metals have rare combinations of high mechanical strength and ductility. Here, we review recent in situ nanoindentation studies (using transmission electron microscopes) on the deformation mechanisms of nt face-centered cubic metals including Cu, Ni, and Al with a wide range of stacking fault energy (SFE). Moreover, in nt Cu with low-to-intermediate SFE, detwinning (accompanied by rapid twin boundary migration) occurs at ultralow stress. In Ni with relatively high SFE, coherent {111} twin boundaries lead to substantial work hardening. Twinned Al has abundant {112} incoherent twin boundaries, which induce significant work-hardening capability and plasticity in Al. Finally, twin boundaries in Al also migrate but at very high stresses. Furthermore, molecular dynamics simulations reveal the influence of SFE on deformation mechanisms in twinned metals.